Mewtwo Strikes Back Retold
by MadDogLucario96
Summary: Retelling of the first movie and prequel to Life's True Meaning. When our heroes get a prestigious invitation to a gathering hosted by the world's top trainer, they think nothing unusual of it. But what happens when they meet a Mewtwo with genocidal intentions? Find out in this alluring tale. Rated T for some language and "other" references.
1. Chapter 1

**Hi guys. I'm back again with that prequel to 'Life's True Meaning' that I promised you. This time I am collaborating with ProcrastinationIsMyCrime and she has been great with ideas and writing. I have seen the first movie close to a thousand times since it first came out, which was a pretty long time ago.**

 **This will also expand on Troy's backstory so you guys can kind of understand him a lot better than I have been doing. PIMC has helped me with doing that and I thank her. I've been kind of just forcing Troy on you guys and saying 'Just roll with it' instead of expanding on him so you guys can relate to him but that has changed.**

 **But for now, let's enjoy this retelling of Mewtwo Strikes Back. Don't own anything except Troy, yada yada yada.**

* * *

Revenge.

That was all that consumed the Pokémon's mind. Revenge against the ones that created him for the purpose of exploiting his power for their own greed. Revenge against those that tried to enslave him for their own benefit.

Standing on the ruins of the laboratory where he was created, a Pokémon called Mewtwo stared out at the seemingly endless miles of ocean that went as far as the eye could see.

He had been created for the sole purpose of serving a man named Giovanni, that he had been cloned from the ancient Pokémon Mew to be stronger than any living Pokémon in the world. The scientists that created him cared nothing for his well being and livelihood but for their own greed and how they could get rich off of what he would bring them. In an outburst of anger, he destroyed the lab and killed everyone in it. Among the still burning remains, Giovanni arrived and convinced him that he could become even more powerful if he had the proper training, saying that the two of them would be partners in this endeavor.

Mewtwo agreed to the terms and soon was placed into a semi-bionic suit that would help him, as Giovanni said it, "focus his powers." Being kept inside the deep underbelly of the Viridian City gym, he was used to help Giovanni take out the challengers at the gym and whatever else he needed him for.

But that was not enough for Mewtwo. He wanted answers as to what his purpose in life was and his purpose for being created. What was this life worth living for? What is the purpose of being a part of this world? How he wanted to know the answer to those questions.

Soon enough, he brought that question to Giovanni. What happened next spiraled things out of control. Giovanni told him that his sole purpose in life was to serve him and nothing else; that he was not a partner but his weapon of war. Mewtwo did not take kindly to those words and destroyed his bonds before flying back to the island that he was created on, destroying Team Rocket's base in the process.

 _'What is my purpose here?'_ Mewtwo asks himself. _'I will find my own purpose and purge this world of all who oppose me, no matter who gets in the way. Soon the world will quake in fear before me. The age of Mewtwo has now begun.'_

* * *

Walking along coastal hills on a sunny morning alone, a brunette man of eighteen silently looked out to the ocean and watched a pod of Lapras swim by in peace.

A family.

Sighing sadly, he sat down on the soft grass and leaned forward with elbows against his knees for a moment before pulling out his wallet and gazing at the crinkled photo of a beautiful woman within it. It'd been three years since he'd last seen her and Troy imagined that it would be many more before he'd ever see her again.

He could remember that year well. Fifteen years old and the reigning Kanto champion for the fourth consecutive year, full of pride for his faithful Pokémon and what they'd achieved together since he was twelve. The news of his mother passing away while he was gone shocked him to the core and it left him questioning many things for a time. Finally after a long time of difficult soul-searching, he'd decided he'd continue battling and training to be the best for his mother's memory. After a time, it wasn't fun for him anymore before finally retiring from it all at seventeen.

It was only when a trio stumbled upon him in his hometown one year later where a boy not much younger than him nagged Troy to help him become a better trainer, but he refused. What was the point of returning to battling when he found no joy or meaning in it anymore? It was only after the rescue of a ten-year-old boy's Pikachu from petty thieves and a talking Meowth that Troy decided to help Ash and his friends. He felt that is was the right thing to do since Ash, Brock and Misty seemed to be well acquainted with those thieves and not arming them with knowledge of how to get out of a bad situation would have been selfish.

He tagged along and consequently witnessed just how persistent Team Rocket were in their attempt to capture Pikachu. Troy, as a result from travelling alongside the three, learned their personalities and clashed with each of them for different reasons.

No matter how many times he tried to drum it into Ash's head to plan ahead during a Pokémon battle, the younger trainer didn't really seem to listen and would grow frustrated when he was outwitted by an opposite. Troy wasn't oblivious to the fact that Ash disliked being called out on making knee jerk decisions, but he was only trying to help Ash. They got on for the most part though and he could see that Ash was making progress as a trainer, albeit slowly because of his resistance to changing his direct-force and type-based battle style. It was a predictable one.

Troy on the other hand was the complete opposite for he constantly changed the way he battled so to keep his opponents guessing. It was what he knew best and had worked well for the more experienced trainers for many years. Having to witness Ash do the same thing again and again grated on his nerves and he found it difficult to resist the urge of pointing it out.

Things with Misty weren't bad, so to speak, but he learned that she was a girl with a strong personality unlike the fan girls he'd had to face during his years as reigning champion. The sight of panties and bras raining down on him, some of them he believed had just come off, and girls screaming their heads off as he entered the arena in the past was difficult to forget and Troy was grateful Misty was nothing of the sort or he'd probably have gone back home long ago.

He got on with her for the most part and although she wasn't aiming to become a Pokemon Master like Ash, they often agreed with Ash's predictability in battle. On the other hand things would go south when their views weren't aligned, leading to Misty trying to shout her opinion across to him while Troy remained steadfast about his beliefs and choices. She wasn't a bad companion, but it was a work in progress.

Brock, out of the three, was probably the one he got along with the most. The rock-type trainer wasn't as hot-headed as the other two and would make an effort to understand the what and why of Troy's reasoning, but there was something he felt was the cause of mild resentment from Brock.

Girls.

Brock chased girls, but girls chased Troy. It was an easy to foresee problem and he couldn't help it. It wasn't like he was trying to taunt Brock about his struggles to find a girlfriend, the fangirls had minds of their own and pursued Troy on their own violation. While it was understandable there was nothing Troy could do to stop them from fussing over how attractive they found him, it didn't take a psychic Pokémon to know that it made Brock jealous.

Getting up off the grass and heading back towards the picnic site, he raised an eyebrow at the plum of dirt rising into the air.

' _Probably Ash battling again. I hope he's mixing up his strategy.'_

Growing curious of how the trainer currently under his wings was doing, Troy picked up the pace towards the trio when he heard the sound of a trainer and the dialect of a Venusaur and Pidgeot further inland.

"You've got this, Bruteroot. Fast but strong! Solar beam!"

' _Who calls their Venusaur 'Bruteroot'? I suppose I've heard worse. You won't catch me calling mine that. I wonder how Venusaur's doing back with Gyarados at home? I ought to let Lucario and Gengar out. They'd like this weather. Lucario would at least.'_

Following the bright light with the only Pokémon he had with him and looking up at the target, Troy spotted a Pidgeot flying nearby and dodging grass-type attacks while combatting them with its own abilities. Observing them for a time with the occasional glance in the direction of Ash's battle, Troy supposed it wasn't a bad way to increase attack speed for something like Solar Beam. Turning away and making for the picnic site, Troy walked off with his Pokémon following beside him, Gengar being a nuisance to Lucario as usual.

"I challenge you, Troy Black!"

Turning around, he saw that it was that trainer and his 'Bruteroot', the Pidgeot out of sight or back in its ball. Getting a better look at the trainer, Troy could see that he was dressed in all red: a red jacket with a yellow patch on the chest, red pants and even red shoes. The only thing that broke the continuation of red was his navy blue hair. He wore a determined and somewhat overconfident look on his face. Lucario grumbled lowly, but a brief touch on his paw quieted him. Raising an eyebrow at the boy slightly older than Ash, Troy stuck his hands in his pocket and stared at him, saying nothing. The certainty waivered on the trainer's face before he took a half step toward.

"You are Troy Black, aren't you?"

He immediately knew this trainer wasn't going to give up until he had his battle with him. He sighed. "Yeah, I used to be." Turning away again and heading for Ash, Brock and Misty, he saw that a Pidgeot stood in his way. Instead of having Lucario or Gengar knock out the bird, he turned back. "And you would be?"

"Corey Slayzer from Vermillion City, and I challenge you to a battle!"

With a shake of his head, Troy glanced to Lucario, who nodded and stepped forward.

"This is going to be good practice for when I get to New Island," said Corey, smirking. "A former champion will get me ready for the greatest Pokémon trainer in the world."

"Hate to burst your bubble, kid," returned Troy. "But I intend to pound you into dust."

"We'll see about that. Go, Bruteroot. Razor Leaf."

The huge grass type fired off dozens of razor-edged leaves towards Lucario.

"Dodge it and use Aura Sphere!" Troy commanded.

Lucario dodged every single one of the leaves before firing off a small sphere of blue energy towards his opponent, scoring a direct hit. Bruteroot cried out in pain from the impact.

Corey gritted his teeth in frustration. "You haven't won this one yet," he said stubbornly. "Bruteroot, Solar Beam!"

Channeling the sun's energy, Bruteroot started powering up for the attack. This gave Troy only a few precious seconds to attack.

"Lucario, Bone Rush!"

Bringing his paws together, Lucario summoned a light blue staff and charged towards his opponent. Lucario gave a loud growl as he swung the staff at the defenseless Venusaur. Hit after hit, Lucario was doing a ton of damage while Bruteroot lost concentration on producing a Solar Beam.

"Let's finish this, Lucario," Troy encouraged. "Use Force Palm!"

The blue staff disappeared and Lucario stuck out his right paw almost instantaneously. A yellow beam blasted out of his palm and collided with his opponent. A cloud of smoke from the collision rose.

"No Bruteroot!"

When the smoke cleared, Bruteroot was out for the count. Lucario smirked slightly at his victory, not needing to celebrate. Corey quickly returned his Pokémon to its Poké Ball.

"Well if I can't beat you on land, I guess I'll have to beat you in the air," he stormed. "Pidgeot, let's go!"

The bird Pokémon flew into the air with a cry, ready to take on its opponent.

"Alright, Lucario. You had your fun. Take a rest," said Troy. Lucario was more than happy to comply and went back over to Troy. "Alright, Gengar. Let's go get 'em!"

No answer. Troy looked around, puzzled by the disappearance of his Pokémon, but there was no Gengar to be found.

"Gengar? Where are you?"

"Come on, I don't have all day!" Corey cried impatiently.

"Uh sorry about that." Troy smiled apologetically. "Gengar! Come out here right now!"

Without warning, Gengar reappeared right in Corey's face. His Cheshire Cat smile nearly scaring him out of his wits.

"Gengar!" He cried.

Corey gave a terrified yelp and fell back to the ground, surprised and startled by Gengar's reappearance. Gengar laughed at his prank. Troy couldn't help but laugh with him.

"Alright, Gengar. That's enough," he chided. "Now let's battle."

Gengar affirmed with a fist and flew into the air with Pidgeot.

Corey growled in anger. "I'm going to make you pay for that. Alright Pidgeot, use Quick Attack!"

Pidgeot flew at Gengar with momentum energy surrounding it. Troy did not have to give a command at all because Gengar disappeared in a blink. Pidgeot stopped attacking, confused as to where its opponent ran off to.

"What is this?" Corey demanded. "Is this some kind of show or something?"

"Hey, I can't help it if Gengar wants to play around." Troy had his hands out defensively as he gave his explanation. "Just how he rolls."

Without warning, Gengar reappeared and prepared to give a Confuse Ray attack on the still-confused bird.

"Above you!" Corey cried to his Pokémon. It was too late however and the attack collided with it. "Use Gust!"

Pidgeot flapped its wings desperately but they were not heading towards Gengar.

"Take a look," said Troy, pointing towards the confused Pokémon. "Your Pidgeot is confused." He then dialed up another attack. "Alright Gengar, now use Shadow Punch."

Black energy surrounded Gengar's right fist as he made a punching motion towards the bird. Since Shadow Punch never misses, it did a lot of damage to the confused Pokémon. Corey could only watch helplessly as his Pokémon took the hit.

"Keep it up, Gengar. Now disappear!"

Without hesitation, Gengar vanished from sight.

"Oh come on!" Corey's patience finally wore thin. "You can't keep doing that! It won't save you."

"I'm not doing it to save myself, silly boy," Troy chuckled. "Just watch. Gengar, use Night Shade."

From out of nowhere, two dark beams rained down on Pidgeot, both colliding with ease. Gengar reappeared, prepared for the next command.

"Now use Shadow Ball!"

A dark ball of energy built up in Gengar's hands before he fired it off.

"Dodge it and use Quick Attack again!" Corey commanded.

His Pokémon did exactly as instructed and dodged the Shadow Ball. It then charged up to go in fast but Gengar vanished again.

"Wrap this up with Shadow Ball!"

Another dark ball of energy came in towards Pidgeot again, this time there was nothing it or its trainer could do and the attack collided with it, sending it crashing to the ground with a cloud of dust from the impact. After the dust cleared, it was clear Pidgeot couldn't go on.

"And that is that." Troy said. Gengar returned to his side, giving him five. Corey returned his defeated Pokémon to its Poké Ball with a look of disgust and frustration.

"You may have beaten me this time," he raged. "But after I defeat the world's greatest Pokémon trainer at New Island later, I will be back for a rematch."

With exhausted Pokémon, the defeated trainer walked away, presumably for a Pokémon Center after the way Lucario and Gengar had trounced Corey's Pokémon so thoroughly. Leaving the area and returning to the trio, Troy was greeted by the sight of Ash praising his Bulbasaur and Squirtle while Misty and Brock watched on from the table.

Seeing the happiness between Ash and his Pokémon, Troy felt a smile creep onto his own face as he walked over and joined the redhead while Brock went over to a simmering dish on the fire. "How'd he do?"

"Predictable, as usual. The other trainer was pretty obvious though."

At the footsteps he looked up and saw Brock shrug slightly as the breeder started serving up lunch. "He wasn't bad, but still needs to think ahead."

The smell of Brock's food was making Troy's stomach grumble as always, but taking the pack off his back and digging out a blue tin can, he approached Lucario and handed him some of Brock's creation for refreshing a Pokémon after battle.

"Here ya go," he ruffled Lucario's head. "Eat up. You did well today, my friend."

Lucario gave his thanks before stuffing his face. Troy then approached Gengar, who was reclining back and basking in the sun.

"Food's on, Gengar. Come and get it."

Gengar sat up and drifted over to where his food sat. With a thumbs up of thanks to his trainer, he started chowing down.

Returning to the table, Troy watched Ash's Pokémon play in the pleasant weather, but couldn't help frowning at the lack of Charizard's presence. Charizard wasn't a bad Pokémon and neither was Ash a bad trainer. In the beginning he'd presumed Ash had mistreated it and Troy wondered if he'd made a bad judge of character about the younger boy, but after a while and seeing how Ash was never abusive with his Pokémon as he'd seen from other trainers with bitter-acting Pokémon, Troy realized that it was something outside of Ash's control.

Well, not entirely outside of his control. He knew the story of how Charizard had been abandoned as a Charmander and it was the key to unlocking the mystery. He'd seen this kind of problem before; a trainer finds an abandoned Pokémon, trains it, evolves it, and soon finds themselves with a Pokémon that suddenly seems to hate them.

No matter what Ash did, this was going to happen and Charizard was going to be nothing but grief for Ash. However the fact that Ash had used Charizard as a Charmeleon to evolve a Paras wouldn't have helped matters between the two. Doing something like that, even though Charmeleon had been more than happy to do it, most likely planted thoughts within the Pokémon's mind that would later fester and make its view towards Ash less than positive.

' _But Ash keeping it inside its ball isn't going to help the matter improve.'_

Suddenly a huge gust of wind blew everything back a few yards just as Troy was about to dig into his food. Everyone fell to the ground as their table was blown sideways.

Looking over, Troy saw a Dragonite standing beside the fallen table with a pack around its shoulder.

"Hey, why don't you watch where you're flying?" Ash asked, rubbing his head.

Dragonite didn't seem to be too concerned with their damaged goods, instead giving Ash a letter from its pack.

"What's that for?" Troy asked. Ash opened it and there was an invitation that looked like a projector. Everyone crowded around.

A woman was projected from the center of the invitation.

"Greetings Pokémon trainers," she said. "I bear an invitation."

"She's really small but really pretty," quipped Brock.

"Shut up, Brock." Misty chided.

"You've been chosen to join a group of Pokémon trainers at a gathering. It will be hosted by my master, the world's greatest Pokémon trainer, at his palace on New Island. A ferry will leave Old Shore Wharf to take you to the island this afternoon. Only trainers with this invitation will be admitted. If you decide to attend, you must reply at once. My master awaits you." She gave one final bow before she disappeared.

"So that's what that trainer was raving about when he said he would be meeting the world's greatest Pokémon trainer," said Troy.

"So should we go?" Misty asked.

"Of course!" Brock exclaimed, yelling right in Troy's ear. "I've got to meet her."

"Ow!" Troy grabbed his ear. "Dang, Brock. You don't have to shout."

"I guess the world's number one trainer wants to challenge me to a match." Ash said, a spark present in his eyes.

"I'm not sure about this, Ash," said Troy. "I sense something foul afoot. Maybe we should just say no and get on our way. You've got more training to do before the Indigo League."

There was a brief silence as Ash seemed to be in thought.

"Nah!" He finally said. "You worry too much. This is a chance to battle with the world's number one trainer."

"I'm still not sure about this."

"Let's take a vote," retorted Ash. "Brock? Misty? What do you guys think?"

"I'm in. I've got to meet that girl!" Was Brock's answer.

"I think it would be fun." Misty replied.

Troy seemed to be in thought, knowing now that he was the lone minority. Maybe he was just being paranoid or maybe he wasn't. There was only one way to find out.

"Alright," he relented. "Alright. I'm gonna back you on this one. But I sure as hell hope you know what you're getting into."

With his approval, Ash checked 'Yes' on the other piece of paper before giving it to Dragonite, who flew away.

* * *

 **A/N: So how was that for a first chapter? Now that you guys have a bit more of a backstory to Troy, what do you think of him? Please let me and ProcrastinationIsMyCrime know so that we can change things or keep doing what we're doing. Drop a review if you don't mind. See ya next time.**


	2. Chapter 2

**Well here we are with the second chapter, folks. Hope you all are enjoying it so far. I've enjoyed writing it for sure. I especially want to thank ctran03931 for his/her amazing review. It really got me even more excited going forward with this story. This chapter should expand on Troy and his interactions with the group. Continue to give me your opinions of him, guys.**

 **So without further adieu, let's find out what's going to happen next.**

* * *

It was well after lunch and the gang was still at the picnic site, Misty was looking after Togepi while Brock was spending time with his Vulpix, making sure she was as healthy as she could be. Ash, on the other hand, was a small distance away, training his Pokémon.

All except one.

Troy was enjoying the sun with his Lucario while it lasted. The weather had yet to take a turn for the worst but if those clouds were anything to go by, there was going to be one hell of a storm later. Gengar, being the mischievous ghost that he was, was back in his Poké Ball for now but no doubt plotting his next stunt. The ghost type always lightened the mood but sometimes the guy would go a little too far with it. Troy blamed Ash's Squirtle for making Gengar go overboard, but inside he knew that it was just Gengar being Gengar.

Although Venusaur was his first Pokémon as a little Bulbasaur, Troy's travel partner was Lucario. However the young man valued all of his Pokémon as good friends who he'd support when they had a tough time and he knew they'd do the same for him. Lucario, Gengar, Venusaur and Gyarados were the Pokémon he'd known the longest and always fought well for him in the past against challengers.

On his belt at the moment were just the Poké Balls for Lucario and Gengar; Venusaur and Gyarados were back home, making sure that no one broke into his house with the help of his other Pokémon while he was gone. Troy frowned at the memory of the time he'd come home once and his boxers were littered all over his room. His worst fears were confirmed when he smelled a female scent on his bed. Girls tossing their own things at him in the arena was bad enough, but strangers breaking into his house to do who-knows-what with his underwear had been a step too far. He'd always left Pokémon at home since, and it seemed to work.

Needing distraction, he went over to Ash and watched what the younger trainer was doing. Currently out of their balls were Bulbasaur and Squirtle; Pikachu amongst them and dashing in random directions as he avoided Rapid Spin and Razor Leaf. Remembering the sounds from Pidgeotto's training earlier, Troy couldn't help but frown at the obvious fact that Ash was avoiding Charizard. That Pokémon had a lot of potential, but right now it was all going to waste.

"Tle!" Squirtle missed the spirited mouse and hit the trunk of a tree. Coming out of his shell, the water type shook his head and took a few steps. "Squir…"

"Pika?" Running over to the tree and standing up, Pikachu looked at the turtle. "Chupi, pikachu pi chu pika?"

"Squrrr. Tle squirtle," it muttered, but looked up and pumped a fist. "Squirtle!"

Bulbasaur wasn't far away and grinned. "Bulba!" This time the Razor Leaf was headed for Squirtle instead of the agile mouse, taking it by surprise.

Soon enough the three Pokémon were back into their routine, and Troy went over to Ash. The boy seemed content and followed the three with his eyes, but not giving feedback as Troy would have done.

"Ash?" He received a nod and continued. "Let Charizard out."

That got him Ash's full attention. "Are you crazy?" He snapped. "Charizard hates me. Ever since he evolved into a Charmeleon, he uses Flamethrower and ignores me."

"Well have you thought of why that may be?" Troy asked calmly. "The only way the two of you are ever going to clear things out is training together."

"Don't you think I'm doing the best I can?"

"Doesn't look that way to me." Troy then took a breath. "Look, Ash. When a Pokémon is taken in by a different trainer after being abandoned by their former one, there are some seeds of mistrust already planted. When that Pokémon evolves while the trainer is still learning, the Pokémon will not respect them. You have to earn a Pokémon's trust and not training Charizard enough does not help you earn his trust."

"What do you know about that?" Ash snorted, turning away from him.

SLAP!

Next thing Ash knew, he was on the ground with a sore cheek. He looked at Troy with shocked eyes. All of Ash's Pokémon protested in anger. Pikachu even went as far as to spark from his cheeks, threatening to shock Troy to kingdom come.

"I do know what I'm talking about!" Troy shot. "I don't hear you calling yourself the ex-Kanto champion."

"Ok guys. Let's all just calm down here." Troy turned sharply, ready to lay into whoever it was. He stopped when it was Brock who said that. Brock placed a hand on Troy's shoulder to calm him down before helping Ash up off the ground. "We're all friends and want to help each other."

Troy took a deep breath, calming down just a bit.

"Ash I'm sorry I slapped you," he apologized. "It's just that Charizard has great potential and I hate seeing a Pokémon not live up to their potential."

"Troy is right, Ash." Brock agreed. "The more you keep avoiding Charizard, the worse the situation will be. The only way a trainer and Pokémon can become one is to train together constantly."

"And you call yourself a future Pokémon Master," snorted Misty with an unimpressed look. Togepi chirped happily, blissfully unaware of the situation.

"Back off, Misty." Ash snapped. He stomped over to where all of their gear was to grab his things. "Let's get going now. We need to get to the port."

Watching the younger trainer return his Pokémon to their balls before walking off with Pikachu faithfully on his shoulder, Troy sighed and grabbed his own gear and followed after calling back Lucario. Brock went ahead and seemed to be talking to Ash in low tones, while Misty walked beside Troy as she carried Togepi in her arms.

He's such a bonehead," Misty muttered while adjusting her hold on Togepi. "How you keep trying is beyond me sometimes."

Troy shrugged, hands casually in his pockets. "Ash needs to figure out when to forget about pride and listen. Someone's gotta do it."

She didn't look too pleased with the blasé way he dismissed Ash's behaviour. "But why should you bear the brunt of it? Ash aspires to become what you've achieved and he scoffed at your words."

"You get used to it," replied Troy with another shrug. "There are a lot of stubborn hotheads in the Pokémon leagues."

"And you're going to make Ash see sense? Good luck with that Troy, you'll go crazy first."

Watching his step as they reached the slopes, Troy glanced ahead and saw that the other two were just walking normally now. "I don't think so, but I will make him see sense. Ash just needs a kick up the ass every now and again and I'm just the guy to give it."

"Right. If you say so," she remarked, still not believing him. "Better you than me. I like my mallet too much, but I normally reserve that to save poor girls from Brock."

"Until they come running to me."

"In your dreams, superstar."

"Oh ye of little faith."

"Whatever."

After a moment of seeing Misty's disbelief, he looked in the direction of town and noticed that the clouds hadn't dispelled in the slightest. If he had to hazard a guess, things were only getting worse. "I don't like the look of those clouds. It's been getting worse since lunch."

Casting a sideways glance at the water Pokémon gym leader, Troy saw her thoughtful expression before her attention was drawn to Togepi for a moment. "I suppose," she replied, but keeping her gaze ahead. "The ferry should be able to handle it though."

It took everything he had not to groan at her lack of concern. None of this seemed right and none of them were noticing the dots as he was.

' _A random invitation to see "the world's greatest Pokémon trainer" at a palace that I've never heard of. It's weird to say the least. I've known the best Kanto trainers over the last few years and this guy pops up out of nowhere. And a palace on an island to boot. It's…suspicious._ '

"We shouldn't go, Misty," he suggested, being a little too forceful. Troy knew that she'd clam up and refuse to actually think about it if he pushed too hard. "That doesn't look like boat weather to me. And I've never heard of this guy."

Turning to her, Troy saw the girl shrug nonchalantly. "Do you expect to know every hotshot in the league, Troy? You've been out of it for a while now."

"What difference does being in the league make?" he huffed, sensing her resistance. "This guy has come out of the blue and he's got a palace on an island? I would have heard about something like that."

Misty didn't reply and only frowned before her face hardened again.

"You gotta admit that something isn't right. Deep down, surely?"

"We'll be fine."

Clenching his fists within his pockets, Troy snapped his head up at the crack of thunder above them.

' _I could have sworn that wasn't there a moment ago.'_

It began to sprinkle just a little bit, before pouring buckets and making the path before them slippery. It wasn't anything he couldn't handle, but the wind soon picked up and almost knocking him off balance. "I don't think so."

"Oh shut up. It's just a bit of water."

Troy's gut feeling was telling him that this was something that they should be heading away from, not running towards. However if he had no chance of swaying Misty then there wasn't a hope in hell in changing Brock's and Ash's minds. The girl-obsessed guy, and an ambitious trainer.

Mentally putting the matter aside for now, he focused on finding shelter from the rain and fast.

* * *

The port was crowded with trainers preparing to go to New Island. They had all been given invitations to take part in a battle with the greatest Pokémon trainer in the world today and wanted so badly to win. If either of them could win, it would mean they would be well on their way to being the greatest Pokémon trainer in history.

All around, trainers were giving their Pokémon encouragement while others were trying to keep theirs relaxed and ready. The storm continued to rage on outside and even the seas were starting to get a little rough, hopefully not enough to stop the ferry.

Bursting through the automatic doors, Ash and company were thankful for the dryness that the port building brought. They were all soaked to the skin with their clothes completely drenched and hair shagging in their eyes.

"Oh Togepi is completely soaked," Misty fussed as she tried to dry Togepi as best she could.

"I told you guys that storm was going to hit us quickly," said Troy. "But does anyone listen to me? No." He then wiped off all the water that had accumulated on his bare body and his tank top.

"I just can't believe how fast it came in." Brock agreed.

Without warning, Pikachu shook out all the water on his fur like a dog would. Ash and Troy stood back, not wanting to get hit.

"This had better be worth all the trouble, Ash." Troy shot. "If it's not, I blame you."

"It will be," replied Ash. "Just relax and have a little faith in me ok?"

"Alright." Troy sighed. Getting a better look around the place, he could see that most eyes were on him. Oh this was just great! He started to hear all the murmurings of 'It's him,' 'Oh my gosh,' and his personal favorite 'I want to rush that.'

"Everyone please listen up!" A voice cried from the gate to the harbor, thankfully drawing everyone's attention off of Troy for a moment. It was Officer Jenny and standing next to her was the harbor manager.

"I'm sorry but I regret to inform you that the 4 o'clock ferry to New Island has been canceled," she said. "The sea is too dangerous for the ferry to navigate."

Everyone reacted in dismay with differing reactions.

"But I've got to get to New Island!"

"What's the big deal?"

"It's just a little bit of rain."

Troy, however, was not quite as dismayed as his companions were. His hunch had been correct. Something very mysterious was going on and they had better get away from it while they still could.

"Ah well. Too bad," he said lightly. He turned around. "Let's go."

"Get back here!" Misty grabbed his arm and pulled him back, perhaps a little too hard because he was on skates for a few feet until he fell to the ground in the middle of the crowd gathered.

Several gasps went through the crowd again as they crowded around him. Several girls squealed while guys just stared in amazement. Troy smiled apologetically and walked back to his companions.

"Carry on," he said.

Officer Jenny gave a confused look before continuing on with her business. "As I was saying, the harbor manager thinks this could be the worst storm ever."

"You must listen," implored the manager, a blue-haired woman who looked to be in her mid thirties. "The prophets have long predicted the return of the winds of water. I prayed that mankind would never witness that deadly storm again."

Troy couldn't help but roll his eyes as she continued. It all sounded like a crock but he knew that something supernatural was going on. That was for sure.

"And that's why the ferry to New Island has been canceled."

"Well I'm going to New Island anyway," said one trainer with brown hair and a cocky look on his face. He wore a light blue tank top and navy blue shorts, red shoes, fingerless gloves in an equal shade of red and dog tags were around his neck. Troy could also see that he had a couple of tattoos: one of a Gyarados going from his wrist to his elbow was most noticeable. "All my Pokémon are water types so we'll just swim over to that island." He boasted.

"The waves will be savage. You won't make it." The harbor manager tried to talk sense into him but it wasn't worth the time.

"Ah whatever. Nothing can stop Fergus P. Richardson." The guy unknowingly introduced himself. "I'm going."

"Alright, if you want to try that stunt and your Pokémon get hurt, you're out of luck." Officer Jenny replied sternly.

"Why is that?" Ash asked.

"We had to close down the Pokémon Center because the nurse at the center disappeared last month," Jenny motioned to a missing person's poster. "If any of you find her, please let me know."

Brock made oogily eyes at the woman on the poster, entranced by her beauty. Though something about her seemed familiar.

"Alright Brock, you want to stare at pin ups? Buy a magazine." Troy dragged him away.

* * *

 **Brock can just never seem to catch a break can he? Looks like Troy's the only one who knows something is wrong. Will the others realize it too before it's too late? You probably know the answer already but it's worth asking. Keep those reviews coming. It motivates me to write more and write better.**

 **FYI me and ProcrastinationIsMyCrime are kind of taking a break from each other for a little bit until she can get going. She's swamped with stuff and I was a little bit pushy so I'm just giving her some space right now until she's good.**

 **See you guys next time.**


	3. Chapter 3

**Hey guys. Back again with a new chapter. Me and PIMC are back talking again and things are good again between us. I hope you guys are enjoying this fic as much as I've been having fun writing it. Now our heroes look to get to New Island. How will they get there? Find out.**

 **Now on with the show.**

* * *

The storm raged on outside. Rain was falling down in buckets and the sea was just as savage as the harbor manager had said; waves were going over the walkway, drenching it in seawater.

Ash and company ran out into this monsoon, despite Troy telling them there was nothing left to fight for anymore, that there was no point now. They stood on a walkway that would normally have a boat attached to it, but there wasn't because of the storm.

The trainer named Fergus called out his Gyarados. He hopped onto its back and the two of them swam off. A girl, who looked about thirteen or so, called out her Dewgong and jumped on its back to follow Fergus.

Officer Jenny called after them, threatening arrest, but her cries fell on deaf ears.

Troy watched the two trainers go off to the horizon, or what could be the horizon considering nothing but dark, threatening clouds hindered the naked eye from seeing it. They did not know what they were getting into, thinking this was something to cement their legacies. He had a worse feeling about this than he did before. It all seemed too good to be true that the "world's number one trainer" was inviting them to his palace to battle with Ash and the two other trainers stubborn enough to brave the weather. There had to be something underlying it.

"What do we do now?" Troy heard Brock ask.

"The world's greatest Pokémon Master is waiting for me," Ash said with that determined expression he always wore. "Let's use our Pokémon to get to that island." Pikachu voiced his agreement.

"Not possible, Ash," refuted Troy. "None of us have Pokémon strong enough to brave a sea as wild as this. It's made worse by the fact that I don't have Gyarados with me, let alone a water type."

"Troy's right, Ash." Misty agreed with him. "We'd be killed if we tried."

"Guess you're right." Ash sighed, disappointed. Pikachu shared his disappointment. "But there has to be a way to get there. There must be."

Troy could feel the stubbornness in his voice. It reminded him of himself, quite frankly. He was also stubborn at that age, drove his parents crazy.

Looking around trying to think of a way to get his crazy friends to New Island, Troy wandered off a little and was surprised to see Corey lingering nearby. Given how he'd been earlier, he'd expected to see the hotshot in flight already but to his surprise when he looked over his shoulder he saw the boy walk up to him.

"I know you don't have a ride over there or you wouldn't be looking so concerned. If you battle me again after New Island, I'll give you a lift on Pidgeot." Releasing the bird and climbing onto her back, Corey continued. "She'd be strong enough for the pair of us. So, yes or no, Troy Black?"

Sighing when he glanced over at Ash, Misty and Brock and seeing the trio getting into a wooden dingy of all things in this storm, Troy turned back to Corey. "Yeah, someone has to keep an eye on that trio of idiots."

"Well, get on, I don't plan to be the last one there," Corey replied rudely, looking restless when he glanced out towards New Island.

Resisting the urge to give him a mouthful, Troy complied and braced himself for the winds Pidgeot would have to fly against.

"Ready?"

"Yeah."

As the avian struggled against the howling winds, Troy began to wonder if this had been a bad idea, but thankfully his worries were resolved when Pidgeot's turbulence steadied and the flight become smoother. Keeping an eye on the other three, he could see that the two people rowing the boat weren't doing too badly against the waves until one that seemed to never stop getting higher collapsed on top of the dingy, capsizing the little boat and throwing all five people out into the ocean.

"No!"

There was nothing he could do to help them, but the helpless feeling didn't subside at all as he was reminded of the fact when his hand went to his belt and he felt only Lucario's and Gengar's balls. He would only be putting them in danger of drowning by releasing either of them.

A hand touched his shoulder, and Troy snapped his head up at Corey. "I'm sorry, all we can do is hold on tight to Pidgeot."

"No! I won't give up on them that easy. Fly over a boat! I don't care which one!"

Corey gave him an odd look but relayed the request to his Pidgeot. Troy could feel the change in its flight from the battering winds. "Why?"

Without hesitation he turned to Corey. "I'll see you later!" And he let go.

"Trooooy!"

But Corey's cry of surprise was soon muffled by the water that surrounded him, forcing himself to the surface and spotting a boat, he swam over and climbed over and raced to the wheelhouse. Ripping the casing off near the wheel and hotwiring the boat, Troy was soon on his way over to where he'd last seen Ash, Brock and Misty. Hoping against hope that their low level water Pokémon could handle the waves.

Speeding along the rough waves in a small speedboat. Troy was dodging and weaving through the rough ocean as best as he could but it was tough. The waves pushed against the boat, soaking him to the bone, but right now he didn't care. He spotted Brock and Misty with Staryu first and not long after found Ash with his Squirtle.

"Are you sure this is safe, Troy?" Misty asked, stuffing Togepi into her bag for safety. "I don't think we should be doing this. It's too dangerous."

"It's better than your idea, Misty," was the dismissive reply. "She hasn't let me down yet. Call in your Pokémon so they don't fall over the edge."

Despite his assuring words, Troy was also very nervous about whether they could get to New Island at this rate. The boat couldn't take much more of this; if one huge wave came over them, they were done for.

"Troy, look out!" Brock pointed up ahead. It was exactly what Troy had feared. A wave, easily thirteen feet high, was about to crash over them.

"Everybody hold on!" He cried as the wave came piling on top of them.

They made it but just barely. Water sloshed around the floor of the boat, everyone felt sore from the force of the wave.

"Is everyone ok?" Brock called out. "No one hurt?"

"I'm fine." Troy called out from the wheel, trying to keep the boat on course after that wave almost knocked them out. The water continued to splash hard against the sides of the boat.

"We're all ok." Misty replied.

Just as everything seemed like it was going to be fine from then on, another wave, this one even bigger than the previous one, came hurtling towards them. There was no avoiding it even if Troy tried to avoid it.

"Uh Troy?" Ash asked.

"Yes Ash?" Troy said in a steady, yet scared tone.

"We're going to crash, aren't we?"

"Yes. Yes we are."

Sure enough, the wave crashed over them and threw everyone overboard. Misty and Brock fell over the sides, Ash was thrown out from the back of the boat, Troy was jerked from the wheel and hit his head on the side, knocking him out cold.

With quick reflexes, Misty called Staryu out to help. It allowed her to grab on and carry her to the surface to search for her male companions. She could hear Brock crying for help before a wave swallowed him. Staryu carried her under the wave to allow Brock to grab hold.

"Have you seen Ash and Troy?" She asked as soon as they resurfaced.

"Not yet." Brock replied. A decent sized wave then consumed them. Misty looked behind her to see Ash riding on Squirtle's back, the salt water stinging her eyes. She grabbed his hand to keep them all together when they reached the surface.

"Where's Troy?" Ash asked. "Did any of you guys see him? We have to find him."

"No." Brock replied.

They all quickly scanned the area around them for their oldest companion, but the waves made it increasingly difficult. He could not have gone far from them and he was a very good swimmer so the waves couldn't have taken him that easily. The smell of salt and the taste of seawater, which had been noticeable already, was overpowering by this point and was only getting worse.

"There he is!"

Ash's thoughts were interrupted by the sound of Brock crying out and pointing to their left. Looking in that direction, he saw a tall body lying in the water unresponsive and drifting away from them. It was Troy. The boat they had just been in was capsized next to his unconscious body and would no doubt sink soon with the way the sea was at this point.

"Quick! Let's grab him before he drowns." Misty urged Staryu on while Ash did the same with Squirtle. The waves seemed to have other ideas though; they became even rougher, pushing the group away from Troy rather than making progress in reaching him. It was almost like the waves were telling them to leave him be.

With dogged determination, the group reached the former Kanto champion. His body bouncing with the waves as they swept under and over him, a small bump on his head was the tell-tale sign of what happened to him. Brock quickly checked his pulse; he was still alive but unconscious.

"He's alright," He voiced. "But he's unconscious. We're going to have to carry him."

The group swam under him to put him on their backs but the weight became too much on them. He was too heavy for them to lift on their own. Brock had an idea at that moment. He'd always wanted to try this but wasn't sure if it would work. Now was the time to find out.

"Ash, give me your belt," requested Brock, taking off his own belt. "I have an idea."

"What is it, Brock?"

"I'm going to knot our belts together and then tie them around Troy's chest before fastening them around us so that way he won't float to the surface if we go under." Brock explained his plan. "Also relieves the stress of carrying him on our own."

"Alright, let's do it." Ash undid his belt and handed it over to Brock. Brock knotted Ash's belt with his and then put the extended piece of leather around Troy's chest.

"Alright now we are going to tie it around us," said Brock as he passed the end of the belt down to Ash. Ash tried to put it into the buckle, the end straining to be put in, but it wouldn't go in.

"I think it's too short." Ash cried.

"Pull harder."

Ash pulled it a little harder this time and he was able to put it in. He then tied it to the tightest setting it could be at.

"Alright, let's go Staryu." Misty instructed.

"You heard her, Squirtle. Let's go." Ash echoed.

The two Pokémon nodded and dove under the water. The added drag of having Troy on top of their backs seemed to slow things down but it wasn't enough to stop them. Everyone held their breath for as long as they could, relaxing their bodies so it didn't cause oxygen to be released. Their lungs relaxed so much that no bubbles came out of their noses.

Then suddenly, everyone started to lose air fairly quickly, forcing the Pokémon to come up to the surface of the water for much needed air. Just as it seems like they are going to run out of air, they reach the surface. What they found was an incredible discovery: the storm had stopped. Clear night sky and bright stars were a welcoming sight after all of the rain. Looking around, they could see the clouds forming around an island into a weird shape that only made the discovery more mysterious.

"Looks like we're in the eye of the storm," observed Brock. "It seems to have started here."

"Then that means this must be New Island." Misty concluded.

A moaning sound could be heard. They all turned to see Troy was now finally awake. He rubbed his eyes as the dizziness wore off.

"What happened?" He asked. "Where are we and where's the boat?" He then noticed the belts around his chest. "And why am I tied up?"

"Troy, you're awake!" Ash cried.

"You've been unconscious for the last while," explained Brock. "That boat is at the bottom of the ocean by now, Troy."

That was what Troy did not want to hear. His confused face suddenly became angry, his face turned red. It looked like he had finally reached his breaking point and he was letting it out.

"Ash, you idiot!" He exploded. "This is all your fault! If you hadn't been so stubborn about getting to this island we would not be like this."

"Troy, I'm sorry ok?" Ash tried to apologize but his apology fell on deaf ears.

"Oh so now you're sorry?" Troy chuckled lightly before turning towards the island. "You hear that, world's greatest Pokémon trainer whom I've never heard of? Ash is sorry! So what. Sorry is not going to get us back to the mainland."

"STOP IT!" Misty yelled. Because of her close proximity to everyone, they all stuck their index fingers in their right, for Brock his left, ears and tried to alleviate the ringing in them.

"So what? I didn't have to come out here with you all. You made me." Troy retorted.

"I'll show you what I'm made of, Troy!" Misty yelled.

"Oh yeah, getting hit by a girl." Troy said nonchalantly before finally exploding. "That's just what we need on some UNCHARTED ISLAND IN THE MIDDLE OF THE SEA!"

SLAP!

Brock gave Troy a good slap in the face to snap him out of his tirade.

"Thank you," he said more calmly. "I needed that."

"We can save all of this for later," said Ash, looking towards the island. "For now, let's get over to the island."

Troy undid the belts tied around him, allowing him to swim alongside the group as they swam over to the fortress-like palace at the island. It gave an ominous feeling of impending doom; the turbines that surrounded it went around hypnotically and the mysterious lighting coupled with the dark clouds created a dark and mysterious aura around the palace.

"Why did I ever agree to this?" Troy asked himself. "I have a very bad feeling about this."

* * *

After swimming for a few miles, the gang finally reached the dock of the island. Lanterns that glowed green made things even more creepy and mysterious than they already were. Ignoring that fact for now, the four of them climbed up onto the dock and did what little wringing of clothes they could manage. Looking at the three of them and Pikachu, it was now that the entire fiasco hit him.

"A rowed dingy? Seriously? I can't believe you made such an idiotic choice. Especially you, Misty. You're a water gym leader for Arceus' sake!" He ranted, the three of them and Pikachu looking embarrassed at the obvious. "When that thing capsized I thought I'd lost you." Stepping forward and hugging Misty, he received nods from the guys before he stepped back.

"It was a bit stupid," Misty admitted sheepishly.

"A bit? A BIT?" Taking a breath and pinching the bridge of his nose, he breathed out slowing with eyes closed. "Let's just go inside. It's _freezing_."

Standing at the doors but coming closer was the woman from the invitation. She wore a long, conservative dress that looked like something out of the late 1800's and headwear that looked like a nun's headdress. The lantern in her hand glowed blue, contrasting with all of the green.

"I bid you welcome to New Island," the woman said, a monotonous tone in her voice. "My master has been waiting for you. Would you kindly present your invitation?"

Ash searched his pockets, getting nervous for a second before finally finding it. He presented it to her.

"The bearers of this invitation may be admitted to New Island." The voice recording of the woman said.

Brock stopped for a second. Now he knew where to place the face of the woman on the poster.

"I knew I recognized that face," he quipped.

"Brock, now isn't the time for autographs." Troy shot him down with a wave of his hand.

"No I'm serious," was the stubborn reply. "She's the missing nurse from the Pokémon Center. I just know it."

"Yeah and I'm really Fabio in disguise." Troy sarcastically replied with a chuckle.

"I'm afraid you are mistaken," the woman said. "I have always lived on this island and have always served my master. Please, come this way. My master awaits your arrival."

As she walked on ahead, the group was not sure whether to follow her or not. They stood on the dock in indecision. Troy took this as an opportunity to make his case again.

"I have a bad feeling about this, guys." Troy said. "Maybe we should cut our losses and leave. It's not like we're going to be missing anything, I mean this is 'New' Island."

"We've already come this far," replied Ash. "There's no going back now."

"I agree with Ash on this one," nodded Misty. "We can't go now. Let's finish the deal."

Them and Brock ran after the woman, leaving Troy in silent thought.

"Hey guys, wait up!" He cried as he chased after the others.

* * *

 **Good no? I really enjoyed writing this chapter. I can thank a friend for helping me with some of the dialogue at the end there, other than PIMC. Be sure to read and review because reviews get me motivated to write again for you guys. Next time, things get even crazier. See you all next time.**


	4. Chapter 4

**Hello everyone and welcome to this next chapter of my interpretation of the first movie. So far you have only heard bits about this master of New Island but now is the time for you to meet him. I really like the collective response I have gotten so I want to say thank you to all of you who have read, reviewed, and favorited my story.**

 **But enough with that. Let's get to what you really came for. On with the show.**

* * *

Muscles tensed and ready to spring into action, Troy couldn't help his restlessness and desire to get out of here. "This is bad. This is so, so bad."

The redhead huffed for a second and turned to him. "Troy, will you please keep your bad feelings to yourself?"

"I can't help it, Misty. Don't you feel it? Something's going to go real wrong real quick," he explained, only to receive a roll of the eyes from her.

His attention was drawn when Brock looked his way, seeming somewhat interested. "How do you know that, Troy?"

"You don't survive doing this as long as I have without knowing when trouble's coming," replied Troy. "It becomes a sixth sense. I know that we are walking right into trouble."

"If trouble may be coming, we will face it together." Ash encouraged with a determined fist.

"All right. Don't say I didn't warn you," Troy shook his head. "Trust me, when it comes to staying alive, I'm rarely wrong about these things. This may be something that's bigger than us and impossible to overcome."

"When we get inside, just keep your mouth shut and let us do the talking," Misty instructed him with a roll of her eyes. "We don't need your negativity."

"Fair enough." Troy conceded with a nod. As they were led to the entrance of the palace by the master's servant, Troy thought he was hearing voices inside of his head. He wasn't sure what they were saying but he could hear them. He must be going crazy.

"There is a great evil here.' One voice said. 'Leave now while you still can."

"Your doom awaits you and your companions."

The voices were no louder than whispers but he could hear them as clear as day, most were masculine with some of them being feminine. Troy had a feeling there were supernatural things happening at this palace, even though he did not believe in the supernatural at all. It was just all the more reason why they should not have come here in the first place.

"Get out of here! Leave this place."

"We dreamed of creating the world's strongest Pokémon...and we succeeded."

Troy turned his head sharply to each side, trying to see where the voices were coming from, but all he saw was the rocky granite walls that surrounded them. That last voice he thought he heard had come faintly through those walls, but there was no continuation so maybe he had just been hearing things.

 _'I must be losing my mind,'_ he shook his head. _'Try to look on the bright side of things. Sunshine and rainbows. Sunshine and rainbows.'_

It wasn't much longer before they stood in front of the large doors that signified entrance into the mysterious palace. They were black, fitting in with the rest of the building, and gave an intimidating aura.

"So what now?" Ash asked.

"Maybe there's a call box or something." Troy shrugged.

Before anyone else could say anything, the doors opened automatically. They creaked as they opened before setting with a low crash. The woman didn't bat an eye as she walked inside, the others following her like lost puppies.

 _'No going back now,'_ Troy told himself as he took a deep breath. 'Let's just do it.'

Walking inside, the entrance hall was one of grandeur: pillars lined with Poké Ball lanterns lit the entire hall, there was a spiraling staircase at the furthest part of the room, and just in front of that was a long table filled with food. There was also a pool of water at the base of the staircase and a large window gave barely a glimpse at the outside world.

The group recognized the three trainers they had seen earlier. They were either eating or making sure their Pokémon were ok. Corey was taking care of his Pidgeot while the other girl trainer was checking on her Wigglytuff. Fergus sat with a bowl of fruit in front of him, untouched.

"Now that you are here, all trainers worthy of an audience with my master are present." The woman said, turning off her lamp.

Ash and friends gave a collective gasp. Only them and the three others? That didn't make much sense, especially because there were so many other trainers back at the port.

"Wait, so only the seven of us are worthy enough?" Ash asked, confused.

"Natural selection I tell you." Troy interjected.

"Aren't we going to wait for the others to come?" Misty asked. "There were so many of them back on the mainland. What about them?"

"Only those brave enough to weather the storm are worthy in my master's eyes," the woman replied. "If you would please release your Pokémon, you may join the others. It will not be long before my master's intentions are clear."

Taking their Poké Balls off of their belts, they all released their Pokémon. Ash calling out Squirtle and Bulbasaur; Misty called out Psyduck and let Togepi out of her bag; Brock: Vulpix. And finally Troy called out Gengar and Lucario, who looked at him with a concerned look.

Lucario could tell something was upsetting his trainer. He had this skittish demeanor, like the smallest noise would cause him to overreact. Lucario placed a paw on Troy's shoulder, asking him what was wrong.

"I don't have a good feeling about this, Lucario," answered Troy. "I feel like we're walking into a trap, a trap that was carefully designed to look like an out-of-the-blue event to bring our guards down and then they'll spring it on us."

With a loud creak, the doors closed behind the group with a slam.

"You see what I'm talking about?" Troy said. "There's something fishy going on here."

Lucario patted him on the shoulder, telling him to relax, before he and Gengar walked ahead with the rest of the group towards the table.

Corey looked up from his Pidgeot, noticing the new arrivals. He smiled as he saw Troy with them.

"I can't believe you jumped off Pidgeot, Troy," he said. "That was ages ago and I was beginning to worry you'd drowned. You probably should have stayed with me instead of battling the waves. I planned on letting you have first dibs on food."

"Meh, I'm not really in the mood for food right now," replied Troy. "Nice to see you too, and thanks for the help out there."

Corey shrugged a shoulder. "No worries. Just give me a warning next time you do something insane."

"Noted."

"Why don't you say hello to the rest of my team? It would be good since we're going to battle again soon." Corey gestured to his other Pokémon. Aside from his 'Bruteroot,' there was a Sandslash, Scyther, Hitmonlee and a Rhyhorn. All of them gave their own cries of greeting.

"Quite a team you've got there," Troy nodded, impressed by their physical condition. "But is it enough to take out Lucario and Gengar?"

Lucario gave a low growl but Gengar was nowhere to be found.

"Oh no. Not again." Troy groaned at Gengar's disappearance. He slapped his hand to his forehead in exasperation. "Gengar, come on out. This isn't the time for pranks."

"You know you really should control your Pokémon," smirked Corey. "If you can't control them, they'll walk all over you."

Suddenly Gengar appeared right in his face just like before.

"Gengar!" He cried as he forced his small arms out.

Corey yelped in surprise, falling back so much that his chair tipped back to the ground. Gengar laughed so hard that tears started coming out of his eyes. He looked at Troy, who had a less-than-pleased expression on his face and his arms folded across his chest. Gengar sighed sadly and drifted over to his side. Lucario gave him an equal stern look and an admonishing.

"I am so sorry about that," Troy apologized. "Gengar just doesn't know when to stop sometimes. It's in his nature."'

Corey got up from the ground annoyed and angry at falling for that again.

"Well, I'll just have to teach him a lesson next time." He snapped. "I don't how he beat Pidgeot because I'm sure you're aware that ghost types are ineffective against normal types."

"I know that but Gengar is not your typical ghost type."

"If you say so."

The roar of a giant Gyarados, almost as big as Troy's, interrupted the confrontation and drew their attention. Sitting in a small pool, water filling in from the wall, were lots of water type Pokémon. A Seadra, Vaporeon, Golduck, Nidoqueen, Tentacruel and finally a Gyarados all gave noises of greeting.

"Those are all my Pokémon," said Fergus from the table, a cocky, arrogant look on his face. "It was no problem getting through that storm," he bragged. "I rode over on Gyarados."

"I hear it takes a lot of skill to train Gyarados," interjected Ash.

"You bet it does, Ash," replied Troy. "After my Gyarados evolved from a Magikarp, it took me forever to get him to listen to me. But I kept at it and he's become one of my most dependable Pokémon. If only you could be that way with Charizard."

"You hit the nail right on the head, amigo." Fergus smiled. "Gyarados is the best. That's why he's my number one partner." Gyarados roared in agreement.

"Hi, I'm Neesha Porter." The other girl introduced herself. She wore a purple sleeveless blouse with tan pants and a Poké Ball necklace around her neck.

"It is an honor to be in your presence, Troy Black," she bowed to him. "Can I have an autograph?"

"I don't do autographs anymore." Troy declined with a wave of his hand. "The requests got a little too weird for me after a while."

Neesha sighed in disappointment. "Aw, that's too bad. Those are all my Pokémon right there."

Her Wigglytuff walked from the table back over to another pool that had water pouring into it from the wall to join its comrades. On land stood a Blastoise, Ninetails, Vileplume, Rapidash and in the pool was the Dewgong she rode to the island.

"Maybe he won't give you an autograph but I sure will," Brock grabbed her hands with an infatuated look. "The name's Brock, Pokémon breeder extraordinaire, and I would happily give you an autograph just for being pretty."

"No thanks," she declined. "I would rather have the handsome ex-champion's autograph than some dork's."

Ash and Misty could barely contain their giggles as Brock was shot down once again. Brock gave Troy an evil look but Troy just put his hands up defensively, like he didn't have anything to do with it.

Taking a break from the action, Troy decided to walk around the room and observe their surroundings. His real intent was actually to survey any exits that they could potentially use in case things went as bad as he thought they would. Those big doors they walked through seemed to be the main entrance/exit.

' _There has to be another way out,'_ he thought as he stared around the grand room. ' _If we need a quick getaway, we need to know where a different exit is.'_

But as he observed more, he could not find anything that seemed like an exit point, save for the spiraling staircase that led upstairs to the top but who knows who used those. Troy sighed and gave up his search. They were trapped and it was going to lead to something bad. He just knew it.

Suddenly the lights went dark. Everyone looked around in disarray, confused by the turn of events. Troy's bad feeling felt even worse now, Lucario and Gengar were sharing his exact same thoughts. Pikachu and Togepi took refuge with Ash and Misty. A bright beam of blue light emerged from the middle of the staircase.

"The time has come for you to meet my master," the woman said. "Prepare yourselves for an encounter with the greatest Pokémon Master on Earth."

Corey, Neesha, and Fergus's Pokémon were prepared for battle, growling in determination and impatience. Troy and the others just stood in stunned silence, like they weren't sure what was going to happen.

A figure started to fall from the ceiling between the staircase, well actually more like floating down. It didn't appear to be human and its eyes glowed blue.

"What is that?" Ash asked.

"I don't know, Ash," replied Troy. "I guess that's the master of the palace."

The figure floated down for a few more seconds until it touched the floor. The blue beam still surrounded it, not allowing the confused trainers to get a good look. Everyone gave awed gasps at the sight before them.

"Yes, the world's greatest Pokémon Master is also the most powerful Pokémon on Earth. Presenting the master of New Island and soon the whole world, Mewtwo."

The lights came back on, revealing the mysterious figure. It was a humanoid Pokémon with a long sweeping purple tail and purple eyes. His face was etched in a permanent glare and his hands had only three fingers.

Everyone stared in stunned silence. This was a joke right? This is a joke. There's no way a Pokémon could end up becoming a master of its own kind. No one could speak.

"This is a joke right?" Troy demanded. "This is a joke. Please tell me that this is a joke."

"Troy, shhh!" Brock tried to silence him.

Fergus broke out of his stunned expression to give his own peace. "A Pokémon can't be a Pokémon Master. No way!"

"Quiet, human," the woman said, but the others could hear another voice with hers. It must have been coming from Mewtwo. "From now on, I'm the one who makes the rules."

"How's it talking?" Misty asked.

"It's psychic." Troy exclaimed. "That's how he's able to speak. It's using telepathy."

Without warning, Mewtwo used psychic energy to grab hold of Fergus. He tried to fight it but Mewtwo was just too powerful for him to break free. He gritted his teeth, refusing to submit. Mewtwo gave a sadistic chuckle before throwing him into the pool of water that his Pokémon resided in.

"He should have just kept his mouth shut," Troy shook his head.

Fergus resurfaced a second later and swam over to the edge. His face was beet red with anger after being thrown like a rag doll.

"No one makes a fool out of me and gets away with it!" He raged. "Get him, Gyarados!"

Gyarados charged out of the pool, ready to carry out any command his trainer made. Mewtwo gave him a stoic look, like it didn't matter what they did.

"Gyarados, Hyper Beam him to the next century!" Fergus commanded with a raging fire in his voice.

Gyarados charged up the attack and then fired it off towards Mewtwo. A force field was brought up, deflecting the attack right back at Gyarados. The attack hit and the sea serpent Pokémon fell back into the pool with a giant splash. It lay unconscious in the pool, causing Fergus to jump back in to make sure his Pokémon was ok.

"Child's play." Mewtwo chuckled, the woman repeating his words. He then turned to her.

"Your use has ended." His eyes turned blue and he waved a hand. Immediately the woman looked like she was going to faint on the floor, Brock luckily was able to make it in time before she could hit the floor. Her headdress came off, revealing her identity. It was the missing Nurse Joy from the Pokémon Center on the mainland.

"I told you it was her, Troy." Brock smirked. "I have an intuition about these things."

"Yeah sure you do," Troy rolled his eyes. "But I will admit that you were right."

"Where am I? And how did I get here?" Nurse Joy questioned, looking around the room.

"You have been under my control for the past month," explained Mewtwo. "I brought you here from the Pokémon Center. Your knowledge of Pokémon proved useful for my plan."

"Who are you?" Brock demanded.

"And what is your plan?" Troy also demanded.

"I am the new ruler of this world. The master of humans and Pokémon alike," Mewtwo explained. "You humans are a dangerous species. You brought me into your world with no purpose other than to serve and obey humans. My storm will create a new world, my world, by destroying yours and everything you hold dear. Once that is accomplished, I will rule the new world."

"So just because you want to hate us, it gives you the right to destroy us all." Troy tried to understand. "Then why are we all here?"

"I needed foolish enough trainers to see if they could try and defeat me. In truth, it was to cast all of you to your doom."

"So you'll save the Pokémon before you'll destroy us?" Brock asked.

"No." Mewtwo shook his head. "Your Pokémon will be destroyed with you. They have disgraced themselves by voluntarily serving humans."

Lucario growled in denial while Pikachu did the same thing. They weren't going to take this weird Pokémon insulting their trainers like that. What would Mewtwo know about the bond between a trainer and their Pokémon anyway?

"So, the two of you say I am wrong? That you are not slaves but friends to those humans?" Mewtwo sneered in disgust. "Then you are just as pathetic as the rest of them."

Using his psychic powers, he lifted them into the air before throwing them back. Ash caught Pikachu but Lucario hit Troy in the chest and landed on top of him. Lucario quickly apologized to Troy as he helped him up.

"Don't worry about it, Lucario. The wind just got knocked out of me." Troy laughed it off. He looked over at Ash to make sure he was fine; he was in better shape than he was.

"Humans and Pokémon could never be friends." Mewtwo said.

"You're wrong!" Troy shouted, his patience wearing thin. "We can be friends. We all work together to make each other better and to help one another. I know that you had a bad experience with humans before but don't let one bad apple spoil the whole bunch."

"He's absolutely right," agreed Misty. "Don't be so angry at all of us just for the sins of a few."

"If you are a Pokémon, than I can catch you just like that," said Corey. He turned to his Rhyhorn. "Go get him, Rhyhorn!"

His Rhyhorn gave a roar as it charged towards Mewtwo with a Tackle attack. Just as he was about to make contact with Mewtwo, Mewtwo stopped it before throwing it back skidding across the table, knocking off everything that had just been there, and resting on the ground.

Corey rushed over to make sure his Pokémon was ok.

"You fool. No trainer can conquer me. My powers are too great for even the most high level Pokémon on Earth." Mewtwo almost cackled in disbelief that Corey believed he could defeat him.

Troy could see Ash was getting that look in his eye, having been with him for a little while he knew exactly what he was going to do.

"Ash, don't do it. It's not worth it." He tried to discourage him.

"Then I guess you wouldn't mind proving that power in a real match." Ash challenged, completely ignoring Troy's warning. He was going to teach Mewtwo a lesson in understanding one's Pokémon.

"Is that a challenge?" Mewtwo asked.

"You bet it's a challenge." He responded brashly.

Troy just slapped his hand against his forehead. This was not going to lead to any good. In fact, it only cemented that it was a trap.

* * *

 **Oh boy. Ash and his big mouth. What's going to happen next? Stay tuned for next time. Until then, read and review. I like hearing other's opinions when it comes to my stories. Keep it up.**


	5. Chapter 5

**Hello all. For all my American readers, I hope you had a great 4th of July yesterday. I'm back with this next chapter in a re-adaptation of the first movie. Right now things are starting to get real. I even have a surprise for all of you at the end. Hope you like it.**

 **So without further ado, let's get this train rolling.**

* * *

"Then I guess you wouldn't mind proving that power in a real match." Ash challenged, completely ignoring Troy's warning. He was going to teach Mewtwo a lesson in understanding one's Pokémon.

"Is that a challenge?" Mewtwo asked.

"You bet it's a challenge." He responded brashly.

Troy just slapped his hand against his forehead. This was not going to lead to any good. In fact, it only cemented that it was a trap.

Mewtwo's eyes glowed blue. Nothing happened but something for sure was happening, everyone could sense it.

"You all have just cemented your fate," he said. "This will be the day my reign started with your foolish wish for a challenge."

"We'll see about that," retorted Corey. "Whatever you have up your sleeve, it won't work on me. I'll squash you like a pathetic bug type."

Just as soon as he said that, three holes opened up in the ground. Rising up from the floor were a Charizard, a Blastoise, and a Venusaur. What was different about these ones were they all have dark lines going across their bodies. The Charizard looked like a tiger with its stripes while the Blastoise had most of its markings on its shell.

"Like most Pokémon trainers, I too began with Charmander, Squirtle and Bulbasaur," explained Mewtwo. "But for their evolved forms, I used their genetic material to create even more powerful copies."

"Clones huh?" Troy commented. "So that's what you were talking about when you said that you were created."

"You are very perceptive, human," Mewtwo nodded. "I was cloned to serve humans and humans alone. But not anymore."

Suddenly a strange sound wafted through the air. Everyone looked around nervously, even the Pokémon, unsure of what that sound was and where it was coming from. The window just in front of the staircase disappeared, revealing the darkness of the outside. Lights flashed on, revealing a Pokémon battling stadium. It looked as grand as the one at the Indigo Plateau if it weren't for the Gothic elements of it.

"A stadium," Brock figured out what was going on. "Mewtwo planned this all along."

"I knew there was a reason why he wanted strong trainers and their Pokémon." Troy said.

Corey growled stubbornly. "Your fake Venusaur can't beat my real one. Right, Bruteroot?" His Venusaur roared in agreement, ready to take on its cloned opponent.

"We'll blow away that Blastoise," Neesha echoed. "Won't we, Shellshocker?" Her Blastoise also vocalized its agreement.

' _Shellshocker?'_ Troy raised an eyebrow at the girl's nickname for her Pokémon. ' _Ah well. I guess it makes sense.'_

"It may not have a nickname but I do have…Charizard." Ash pulled out a Poké Ball before throwing it. "I choose you!"

The fire dragon emerged from its ball with its eyes closed in an uncaring manner. They snapped open, glaring at Mewtwo. The two stared at each other for a few seconds before Charizard fired a Flamethrower at him, surrounding him in fire.

"Charizard, I didn't say start." Ash was surprised at his Pokémon attacking without him telling him to. Troy slapped his hand against his forehead again. He told Ash this would happen if he didn't train Charizard enough, but no. Ash just did not want to listen to him.

Though still surrounded by fire, Mewtwo used Psychic to bring up some of the water from the pool in front of him to stop the fire. Steam rose as the water made contact.

"Your Charizard is poorly trained," he shook his head.

Charizard gave a threatening growl, spitting out a bit of fire to symbolize his readiness for battle.

Ash breathed in concentration. This was going to be a tough battle but he was ready for it. This is what Troy had been training him for and it was time to show it.

"You see what happens when you avoid training with Charizard?" Troy nagged. "I keep telling you that avoiding him is just going to create more problems. You need to train with him more to get him to trust you."

"I know what I'm doing, Troy." Ash snapped, tired of Troy telling him this. "You're just going to have to trust me on this."

Everyone walked into the stadium, standing at the near end of the stadium while Mewtwo and his clones went to the other side.

"So which of you will challenge me first?" Mewtwo challenged. "Or are you all too afraid to take me on?"

Bruteroot stepped into the arena first and gave a cry of determination.

"I underestimated you last time but it won't happen again." Corey cried before pointing a finger at Mewtwo. "Prepare yourself for a challenge with the best trainer in Vermillion City outside of Lt. Surge, Corey Slayzer."

"Look, Corey," Troy tried to talk some sense to him. "I think it's time you thought about this for a second. You couldn't even beat me so what makes you think you have a chance now to beat Mewtwo? It's what he wants."

Corey shook his head. "Just watch and see," was his stubborn reply. "This is what I'm going to do to you when we have our rematch. Your victory over me was just a fluke and I'm going to prove it."

Troy just shook his head in disbelief. He had encountered a number of those kinds of trainers throughout his days of traveling and battling. They think they're so good and so strong that they can defeat him but always come up short when it's time to put their money where their mouths were.

Mewtwo's Venusaur stepped into the battling arena opposite Bruteroot. The time had now come.

"You can attack first," Mewtwo granted, though something about it seemed like he wanted it to happen.

"Gladly," nodded Corey. "Go Bruteroot. Razor Leaf."

' _Just like how he started against me,'_ Troy observed. ' _If he's as good as he says he is, he would have done something else.'_

Razor-like leaves shot out from under the flower on Bruteroot's back towards its opponent.

"Vine Whip." Mewtwo commanded.

Mewtwo's Venusaur shot vines from under its flower towards the Razor Leaf, repelling all of the leaves away from it just like that, before picking up Bruteroot with the vines. Bruteroot gave a displeasured cry as it was lifted into the air. Mewtwo's Venusaur then threw Bruteroot back into the room they just came out of, a resounding crash echoed throughout the stadium.

"Bruteroot!" Corey cried, running towards his Pokémon to make sure it was ok.

"Oh yeah, you sure showed him, Corey." Troy laughed sarcastically. "I'm so scared. Just the thought of going up against you, knowing what you can do, has me shaking in my boots."

"Looks like I'm up," Neesha stepped forward. "Go, Shellshocker."

Her Blastoise stepped into the arena to take Bruteroot's spot. Mewtwo's own Blastoise stepped up as well.

Neesha did not waste any time before calling her attack. "Shellshocker, Hydro Pump!"

Using the twin guns on its shoulders, Shellshocker fired the powerful water type attack but its opponent used Rapid Spin, rendering the attack useless. Mewtwo's Blastoise then collided with Shellshocker in the chest, sending it back into the barrier keeping the stands from the arena.

Neesha quickly ran after her Pokémon, copying Corey.

"Ash, I think now is the time to run and not be a hero." Troy tried to talk some sense into Ash once again.

"He's right. Those clones are too powerful." Misty agreed.

"I'm not giving up," he stubbornly replied. "I've come too far to just give up like this."

The other Charizard stepped into the arena, firing off a Flamethrower in a challenging gesture.

"Charizard, use your speed, not power, and you'll win." Ash instructed. Charizard shot a flame to show his understanding. "Alright then go!"

With that, Charizard flew into the air, his counterpart flying off with him after dodging a Flamethrower. What may look like an even bout at first glance proved to be a total mismatch. Whenever Charizard would fire off a Flamethrower, trying to get a hit, his clone would move too quick and hit him with a tackle.

"Can't Charizard move any faster?" Misty demanded.

"The clone is too fast." Brock replied, staring in awe of the speed of Charizard's clone.

Troy and his two Pokémon also stared in awe at just how powerful and quick the clones were. They were faster and stronger than any other Pokémon alive. It was amazing what the power of genetics could do.

After continuously trying to land a hit, Charizard was starting to get impatient. He tried to move closer to his opponent this time but that proved to be a fatal mistake. As soon as he got in, his clone grabbed him around the neck and dragged him down in a Seismic Toss.

Ash stared in horror as his Pokémon was flown towards the ground. "Charizard's in trouble."

"Finish him." Mewtwo encouraged the clone Mortal Kombat-style.

The cloned Charizard tightened its hold on Ash's Charizard as they neared the ground, coming in hot before dropping Charizard on his head. It then flew up with a smirk on its face and flew back to Mewtwo.

By some miracle, Ash's Charizard stood up and roared in determination…before dropping to the ground unconscious. Ash quickly ran to his Pokémon's side, making sure he was ok.

"Victory is mine," Mewtwo sneered. Out of nowhere, three black Poké Balls appeared above him. "Now, as the victor I claim my prize: your Pokémon." The three balls flew towards the defeated Pokémon and captured them, leaving the three trainers in shock and disbelief.

"What are you going to do to those Pokémon?" Misty demanded.

"I will extract their DNA to make clones for myself," explained Mewtwo as he made even more balls appear. "They will remain safe on this island with me while my storm destroys the planet."

"You can't do this!" Brock exclaimed.

"This is outrageous." Troy agreed. "Why should our Pokémon stay with you when you just said that they would die with us?"

Lucario growled in agreement, standing in a threatening stance.

"Because with all of you gone, they can be free. With no humans left in the world, the clones will live on and this planet will belong to Pokémon alone."

Ash stood in the middle of the arena in defiance. "We won't let you do this, Mewtwo." He cried.

Mewtwo's eyes glowed blue. "Do not attempt to defy me." He picked Ash up with his powers and threw him back, sending him crashing into Troy.

"Ow." Troy groaned as Ash landed on top of him. "I think you bruised something, Ash."

"I'm sorry, Troy." He apologized, helping his mentor up. The two dusted themselves off.

"This is my world now," said Mewtwo before he sent the balls off. "Your reign has ended."

Realizing the gravity of the situation, Ash and company ran back into the entrance hall, trying to escape the palace and protect their Pokémon. Soon the sight of Pokémon being captured became a regular occurrence.

Fergus could only watch helplessly as all of his Pokémon were captured. Corey tried to do whatever he could to keep the balls away, his Scyther slashing at them, but it was no good as his Hitmonlee and Scyther were captured along with Sandslash and Rhyhorn. Neesha did the same as Corey, swatting balls away from her Pokémon, but all were captured.

Next to the pool, some pillars opened up to reveal a passageway that the balls all flew down to after they had caught their catch.

Troy ran towards the doors with his two Pokémon, trying to get out of there. They banged on them to try and force them down but it was useless.

' _What are we going to do?'_ Troy asked himself. ' _We can't get out but I must protect Gengar and Lucario. They are my life and if anything happened to them, I can't forgive myself.'_

An idea hit him. How about Gengar tried going through the doors and open them from the outside? It had to work.

"Gengar, I've got an idea," he said. "Try flying out and opening the doors that way."

Gengar nodded with his hand in a fist. He prepared to go into his ghost mode and fly outside…until a ball captured him and flew off towards the risen pillars.

"NO! Gengar!" Troy cried. Lucario also gave a distressed cry as his comrade was captured. Troy looked at Lucario with desperate eyes. They had to protect the others now. They ran back towards the action, Lucario used his Aura to dodge every ball that tried to capture him.

Ash had recalled Squirtle and Bulbasaur, thinking that if they were in their Poké Balls they wouldn't get captured, but the balls caught his Poké Balls instead. Brock and Misty tried running off with their Pokémon but Psyduck and Vulpix were captured very quickly. Misty had stuffed Togepi in her bag.

Pikachu was dodging everything as fast as he could but it was getting tough. Standing on the table, Pikachu was surrounded. Ash took the blows from the balls trying to get Pikachu to give him time to run.

"Lucario, protect Pikachu by using Bone Rush!" Troy ordered. Lucario did not hesitate to follow that order and quickly followed the small yellow mouse. A blue staff emerged from his paws and Lucario carried it, destroying any balls that tried to capture Pikachu.

Pikachu ran up the staircase that Mewtwo had come down from to try and escape, Lucario following him. The balls hounded them like flies, never leaving them alone until the two Pokémon were captured. Pikachu shot off a Thunderbolt to take down the balls that would surround him and Lucario, giving Lucario a hand.

Ash and Troy ran up the stairs to retrieve their Pokémon but Ash slipped and almost fell off the stairs. He managed to grab on to the ledge before he could fall into the water below.

"Troy, help me!" He cried, his grip slipping.

"I'm coming." Troy quickly moved to help him up. Using his strength, Troy pulled his friend up. "You ok?"

"I think so," Ash nodded. "Come on, we have to get Pikachu and Lucario before those balls do."

Troy nodded and the two of them ran after their Pokémon.

A few flights of stairs above them, Pikachu shot off another Thunderbolt before dropping from exhaustion. Lucario encouraged him to try and get up but Pikachu just laid there. Seeing balls swarming around them, Pikachu and Lucario dodged them but they were being pushed back to the ledge.

"Lucario, look out!" Troy cried.

But it was too late. Lucario and Pikachu fell off the ledge and towards the pool below, the balls chasing after them to make one final attempt at catching them. Ash and Troy jumped off the flight they were on to get their Pokémon. Just as Troy was about to grab Lucario's paw, a ball came up and captured him, same with Pikachu. Ash and Troy grabbed the balls that their Pokémon were captured in before they could get away.

SPLASH!

The two fell in the water below, the balls getting away from them. Swimming up to the surface, they climbed out of the water and ran towards the pillars, which were just about to close, and slid down the passage.

"You're not going to get Pikachu/Lucario!" The two of them cried.

* * *

Tumbling out of the passage and finding themselves on a conveyor belt inside a study or lab of some kind, the pair didn't allow themselves to get distracted at the sight of two black Poké Balls just shy of their reach. Jumping up and chasing after Pikachu and Lucario's balls Ash and Troy soon had a grasp on their respective ball, but found themselves fighting against dozens of electronic arms trying to pry the balls out of their hands. Within moments, the arms were grabbing onto anything and everything to stop them from escaping, which only made their adrenaline kick in and fight harder.

Using all the strength they had, going as far as to use their teeth to break the arms, the duo managed to go back out the way they'd come, but not without a few small electronic burns from the robotic arms sparking wildest as they fought.

Once off the conveyor belt and catching their breath, Troy was relieved to see Lucario's ball release the blue jackal in front of him, Lucario looking fine from the ordeal. At the cries of Ash's Pikachu, he glanced over and saw that the same had happened for them. He and Lucario embraced each other, Troy hugging him so tight that he never wanted to let him go.

"I'm so happy you're alright, Lucario," he said. "I don't know what I would have done if I'd lost you."

Not sure how he was going to get out of this laboratory, he looked to Lucario after breaking their hug before walking around and seeing the computer along the wall, as well as the tubes that now contained copies of everyone's Pokémon.

Using the bench to steady himself from the surprise of seeing the clones, Troy nearly jumped out of his skin at the sound of a voice coming from the computer. Turning to the screen and witnessing the sight of something they didn't understand, Ash and Troy watched anyway but within a few seconds of the video beginning, they were distracted by their companions' cries.

"Pikaa!"

"Caarrr!"

Racing after their Pokémon once again, this time suspended in the air towards the machine by those robotic arms, Ash and Troy dove towards them and grabbed on before pulling them back. But instead of being pulled in like last time, the two trainers landed on their backs after Lucario and Pikachu yelped before landing on top of Troy and Ash, knocking the wind out of Troy, and Ash to a lesser extent.

A feminine robotic voice mentioned 'analyzing', but the projection on the wall of two lines that soon became the shapes of Pikachu and Lucario. Behind them was the sound of many bubbles and the four of them turned in time to see second copies of the mouse and jackal appear in one of the many green tubes.

Watching his Lucario with interest, Troy witnessed the loyal Pokémon looking at the two with an unsettled expression before Ash broken the silence.

"Clones."

"Hmm."

Feeling edgy himself after seeing just what this machine was capable of, Troy spun around at the sound of a high pitch squeak and spotted a pink tail for a moment before it was out of sight, but he didn't have any time to dwell on what he thought he'd seen.

A voice from the computer was this time a hasty male and disaster could be heard in the background, drawing his and Ash's attention once more.

"I haven't got much time. I pray this record of our experiment survives. A year ago, we discovered the remains of the ancient Pokémon: Mew. There was sufficient material to replicate Mew but Giovanni, who funded our project, insisted we try to design super clones that are more powerful than any living Pokémon. Many attempts failed but finally our experiments proved successful. We produced a living Pokémon; we called it Mewtwo. But for some reason the creature's anger is out of control. With its psychic powers it is destroying our laboratory. We dreamed of creating the world's strongest Pokémon...and we succeeded."

Looking around the lab with new eyes, Troy noticed how the place looked like a new version of what had been on the screen. Stepping back and taking a breath as he glanced at the ceiling and imagining just what could be going on up there, Troy knew in his heart that Mewtwo was beyond reasoning and if there was any way to stop the feline from taking its vendetta too far, he would do it.

Lucario seemed to notice the change in Troy and walked up to him until they were face to face, the jackal nodding before putting a hand on his shoulder. "Lu…."

"We'll get through this Lucario," Troy promised, before his eyes landed on a copy of Gengar near Lucario's right shoulder. "We'll get through this."

"So Troy what's your plan for getting us out of this?"

Troy was snapped out his thoughts and turned to Ash, unable to believe the gall the younger trainer had to expect him to solve his problems. "Excuse me?"

"That's why you're here. You're the Master of the Thinking Stuff."

With a humorless chuckle, he went over to the rookie, Lucario standing close by. "Oh I see," he remarked lowly, seeing Ash shift slightly but not backing away. "Now I'm the Master of the Thinking Stuff. Opposed to five minutes ago when I was trying to figure out a solution to this problem. But then something happened; someone, who will be anonymous, ASH! KETCHUM! Decided to challenge a Pokémon to a battle then said Pokémon catches all of ours. And here we are, while that homicidal maniac is preparing to use his storm with the simple intention of destroying our world and killing us all."

Right now he just wanted to throttle the idiot into next week, silently questioning why he'd been helping this kid become a better trainer the past few months.

Ash was now a little nervous but there was no change in his expression for help. "Look, Troy. Let's just calm down here."

That just made him mad at Ash all over again. The impulsive twit was telling him to calm down and think things through. "I can't be calm. No, no, no. I'm the Master of the Thinking STUFF! And I have to help you. You, the Master of the STUPID STUFF! You want a solution? I'll give you one. You see that control monitor over there? In the true Ash Ketchum style, I'll just throw a Poké Ball at it."

Troy rarely let his temper get the better of himself but right now he simply didn't care, and this unknown side of Troy was truly frightening Ash. "Troy, you don't know what you're doing."

"Oh but I do!"

And true to his word, Troy tossed a Poké Ball in the direction of the machine without looking, and to both of their surprise there was the sound of a Pokémon followed by the ball wobbling thrice before dinging to signify a capture.

"What…?"

Picking up the ball and he was about to see what he'd unintentionally captured, but Troy's gaze snapped up at the movement within the tubes, where the dozens of Pokémon emerge through the tubing when the lab was beeping at an increasing pace before leaving the laboratory as a group.

Above their heads was an explosion where the black balls fell to the floor, releasing their contents. From Wigglytuff to Gyarados, all of the originals were back and the sight of Gengar in a good condition was a relief. Troy and Lucario ran over and embraced Gengar, happy he was ok.

"Gar, geng gar ge. Gengar!" the mischievous Pokémon spoke with a tone of promise before disappearing.

Troy could only shake his head, and looked in the direction the clones had gone. No doubt the place Gengar had gone.

Right now, Gengar was basically the only Pokémon that could help them, but Troy didn't let himself be lulled into a false sense of security. Mew was a legendary Pokémon, and the super-clone Mewtwo would no doubt be equal it not stronger than Mew. Gengar wouldn't be strong enough to defeat Mewtwo. They'd need a legendary to defeat a legendary.

With Mewtwo bent on ridding the world of humans and original Pokémon, the only result Troy could see was death, no matter what they did.

Troy's thoughts were interrupted once again, but this time by a voice entering his mind. A voice he'd dreaded since learning of the clone's plan.

"Humans, you have served your purpose. I am sparing your lives…for the moment," it informed them. Ash looking edgy before rising to his feet, looking around at the original Pokémon in the laboratory with them. "But you cannot escape your fate, the hour of my vengeance draws near. Behold, with Pokémon and humans eliminated, the clones shall inherit the world."

"Dat's not good!" a familiar voice cried, its owner emerging from a manhole on the floor, running around and settling himself on the keyboard of the computer. Jessie and James not far behind.

Ignoring Meowth, Troy turned to Ash with a grim expression. "There's but one thing we can do, and even then things look bleak." Turning to the group as a whole, he looked at each Pokémon slowly. "They may be clones, but we have something we all treasure. Family, friends, homes, memories. Don't let the unknown stop you from protecting what's important. This is a fight for our lives, a fight for our way of life. So will you stand and fight or just let this maniac destroy everything we hold most dear?"

The thirty something Pokémon around them unleashed cries of determination, but it was the appearance of one Pokémon above them that stunned all into silence.

A white long-necked quadruped with an underbelly of grey, one golden cross-like wheel around its torso. It looked like a deer.

"Your willingness to protect, although the odds are against you, is a noble deed." The Pokémon spoke. It sounded male with its mystical voice. "Alone your efforts would fail, but I shall be by your side. I shan't allow this psychic upstart to destroy our world. The one I worked so hard to build and help flourish."

Bowing to the Original One, Troy nodded silent thanks and watched Arceus lead the way to the light that was streaming into the laboratory.

"What Pokémon is that, Troy?" Ash questioned, a little too loudly.

The Original One turned its head, making eye contact with Ash, which didn't cow the young trainer. "I, Ash Ketchum, am Arceus, and also the one who created this world. I shall help you defend it, Chosen One."

The inexperienced trainer bowed his head a little, before Arceus focused on their path, at which time Ash turned to Troy and mouthing the words 'Chosen One' silently.

Troy himself had no idea and could only shrug. Right now he was too grateful to look a gift Ponyta in the mouth. The Poké Ball he'd thrown in the lab was still in his hand, and if he had a clone inside he had no intention of making their fight any harder than it already would be. Lucario would have two clones to face, as would Pikachu, so any way that he could help his companion and trusted Pokémon he would do so. Clipping the ball to his belt, Troy gasped in surprise when the Pokémon inside released itself to reveal a small, pink, feline Pokémon.

Mew.

"Meeew," it squeaked happily before floating over to Arceus' side as the group emerged out onto a well-lit stadium where Mewtwo and his clones stood, staring down the trainers and Nurse Joy.

* * *

 **WHAT?! Troy caught Mew by accident? And Arceus is now here? What is going on? Well that was certainly a lot thrown your way but I hope you guys enjoyed it. The next chapter is when the shit hits the fan and things just go from there. Keep giving me feedback on the story. I enjoy getting it from you guys because it helps me become a better writer.**

 **Stay tuned for the epic confrontation of all time. See you guys later. Drop a review if you don't mind.**


	6. Chapter 6

**Hello again everybody. It is time for the epic confrontation of all time to happen. I was so excited about this chapter that I just wrote and wrote until it was done. I also give PIMC plenty of credit for her hard work on this too. Can our friends convince Mewtwo to stop his madness? Or will Mewtwo achieve his goal of world domination? We will find out shortly. Hope you all enjoy this chapter. Prepare for major sadness by the way.**

* * *

Standing on opposite sides, the two armies threatened to clash at the drop of a hat. On one side were the clones led by Mewtwo, the other were the natural-born Pokémon led by Ash and Troy along with Mew and Arceus. One bent on world domination, the other fighting to preserve the world the way it is.

Troy stood shirtless, exposing his well-built upper body and many tattoos, and a black bandana around his head. It was time to stop running now and do what was right. He had been running for so long from everything that he'd forgotten what it was like to stand up for something that he believed in.

The time had now come.

Arceus floated in the lead position, keeping a keen eye on Mewtwo and his super-clones. All Pokémon were the same in his eye, but no Pokémon, cloned or not, was going to destroy the world he worked so hard to build and get away with it without him having a say about it.

"Stay this madness," he implored, witnessing the purple psychic size him up with bitter eyes. "I understand your anger, Mewtwo, but this must end."

"Who are you?" Mewtwo carelessly asked, wondering what this strange Pokémon was, intrigued that it was different from the others and also had a telepathic ability.

Arceus moved forward slightly, as though to display a sense of authority before it spoke. "I am Arceus, the Original One," replied Arceus. "I am responsible for creating this world and all of these Pokémon. For eons, I have watched over the realm of Earth from my own dimension but you have forced my hand."

Mewtwo looked at him with an uncaring expression. "Why should I care? I am not of this Earth so I have no reason to obey you. This world belongs to me now."

Undeterred from trying, the Original One pressed the matter, attempting to make the vengeful clone see sense. "Your anger towards humans and yourself blinds you. What will you have left to fight for when you accomplish your mission?"

"That is none of your concern. It is useless to try and stop me from achieving my destiny."

From the corner of Troy's eye, Ash stepped forward but not out of reach of Troy's hand that now rested on his shoulder. "It doesn't have to end like this, Mewtwo," Ash interjected. Although the kid may not know it, he wasn't helping matters by butting into the conversation between legendary and clone.

"We'll take him together," Troy whispered to his apprentice. "You take the Pokémon on the left and…"

"I'm taking him now!" Ash ran towards Mewtwo after turning his hat backwards, ignoring what Troy had said.

"No Ash! No!" Troy tried to get him to stop but it was like trying to stop a stampede of Tauros. It was impossible.

Ash rushed with his hand clutched in a fist. With a determined cry, he punched Mewtwo in the chest, only for a force field to appear and knock him back. Like the determined cockroach he was, Ash got up and tried to go for another punch but Mewtwo halted him with his psychic powers. Without hesitation, Mewtwo sent him off flying towards the stone structure hanging over the battlefield. Troy couldn't look because he knew it wasn't going to end well.

However a high pitch squeak made Troy look up as Ash was about to hit the structure, but a pink bubble appeared, stopping him from crashing into it and getting seriously injured, even killed.

Mewtwo stood shocked. Where did that bubble come from? That didn't matter for right now because he still had other problems to deal with.

Troy stepped forward this time in defiance. The look in his eyes would have scared even the toughest Pokémon. It was a cross between pissed off and an animalistic state.

Even the presence of Arceus wasn't deterring Mewtwo from delivering his hate, all Troy could do was try and save his home; this world. "You want to destroy the world? I won't stand aside and just let it happen." He said, bracing himself for anything after the way Mewtwo had disposed of Ash.

The tension in the air was thickening and the psychic instinctively levitated himself just off the ground, arms slightly out to the sides and ready to use his powers. "And who would you be?" Mewtwo asked, the fine hairs of his fur standing up at the human's statement.

Who was he really? In retrospect, right at this moment he was equivalent to an infant; limited in what he could do. "No one special. Just former Kanto champion, Troy Black," was Troy's nonchalant reply. He was beyond the point of self-preservation now. "You may have beaten the others but you won't beat me. I won't let you get away with this as long as I am still breathing." Hearing the steps from his flank, Troy knew his trusted companion felt the same. "You ready, Lucario?"

Lucario stepped into sight with a determined growl and a sheen of defiance in his eyes, ready to fight alongside his trainer once again.

"Foolish human." Mewtwo remarked with little care, rising further but moving towards his clones without taking his sight off the humans and their slaves. Again he used his psychic powers to pick Troy up, but this time he tossed the human to the side and out of the way. Troy crashed into the stone barrier separating the stands from the battlefield, his whole body feeling like he did a back flop in a pool: everything hurt and his head felt like it got hit by a sledgehammer. His body collapsed to the ground in a bruised and cut heap.

Lucario was growling up a storm at the sight of his attacked trainer. How could that Pokémon just do what he did to Troy? It was not going to go un-avenged so long as he had breath in him.

"Troy!" Brock and Misty immediately rushed over to him, checking to see if he was alright. His entire back was scraped and cut while little bits of stone were stuck in the skin.

"Are you ok?" Brock asked.

Troy tried to hoist himself onto his knees by pushing his arms up. Once that was accomplished, he dragged his knees up so that he could stand. He swayed a bit, almost falling over, but Misty and Brock kept him up.

Mew appeared to Ash, popping the bubble that she had created for him. He fell onto his ass rather roughly.

"Ow," he cried, rubbing his behind. "My ass."

Mew laughed at him falling on his behind.

The sound of laughter pierced the stadium's silence and all looked to her; Mewtwo, Arceus, Troy, the gang, and the various Pokémon below.

She created another bubble so she could bounce around on it joyfully. This lasted only a few moments as a Shadow Ball attack came in and destroyed it, causing her to fall back. Mewtwo fired off even more Shadow Balls in her direction but she dodged them all, giggling mischievously after dodging every single one.

Everyone stared in disbelief at Mew's appearance. They had never seen a Mew before so it was a sight to behold.

"Mew," said Mewtwo, finally getting to see his original self in the flesh. "So we finally meet. I have been looking forward to this for a long time. I may have been cloned from your DNA, but I will prove that Mewtwo is more powerful than the original. Superior in every way."

"No," said Arceus, floating in front of Mew. "If you want to destroy this world, you will have to destroy me," he informed Mewtwo, intent on defusing the situation if at all possible by this point. "I am the one who created it after all."

Down below, Misty and Brock were in awe of the Legendary Pokémon. They had never seen anything like him before in their lives.

"What is that Pokémon?" Misty asked Troy, kneeling beside him and glancing at his cuts briefly, eyes soon back on the Original One.

"That's Arceus," he explained. "He's God of all Pokémon. He created the world and all of the Pokémon in it. He's come here to stop all of this along with Mew."

Rising until level with Mew, Mewtwo saw Arceus as nothing but a pest. "Move, you fool." Mewtwo shot. "My business is not with you. My sole goal is to prove that Mewtwo, not Mew, is the most powerful Pokémon on Earth. It is Mew I shall defeat."

Mew stepped in front of Arceus, accepting Mewtwo's challenge. She was not going to let this clone with an inferiority complex talk to her like that. She convinced Arceus that this was not his battle to fight.

"If that is your wish, Mew. I will step aside and let you fight." Arceus bowed away from the two, although it pained him to do so. He descended until he was over the group of Pokémon, his desire to protect all life while Mew moved towards Mewtwo to begin what he was unable to prevent.

"This world is too small for the two of us." Mewtwo pursued Mew, who'd flown away from him. Shadow Ball after Shadow Ball was tossed towards Mew without landing a single hit. All everyone could do was watch. Arceus had no choice, for Mewtwo had his eyes set on Mew, to stand between them and be the epicentre of a fight would cause more harm then good.

The clone paused for just a moment, hovering out in the open and daring his original to attack. "Why do you run from me? Are you afraid to find out which of us is greater and more powerful than the other?" he taunted, building another Shadow Ball between his hands.

Flying out from behind a pillar, Mew tried to escape Mewtwo once again, but this time Mewtwo was able to land a Shadow Ball, sending Mew flying into the dark night sky. He chuckled, finding it pathetic how easy it had been to prove his strength.

Everyone gaped in disbelief and horror, unable to comprehend the fight they were witnessing. Rising from the ground, Troy wouldn't deny his concern for the well-being of his new Pokémon, although it'd been an accident that he caught the Legendary.

Suddenly, the Shadow Ball that had been tossed since what felt like forever flew back into the arena. Caught off guard and without enough time to react, Mewtwo was hit by the attack and sent crashing into the stands, sending debris flying at the high impact. Gone was the innocent expression from Mew's face as she came flying back into the arena confidently, thinking she had won.

Underneath all the smoke from impact, a blue force field broke through and vanished, revealing a slightly bruised and battered Mewtwo.

"So you do have some fight in you?" He challenged. "But I don't have time for games. My destiny is at hand. Who will rule this world? My super Pokémon or your pathetic, weak, inferior Pokémon?"

Stepping forward towards the bitter clone, Arceus finally strode forward after being all but forced to watch this fight. This was his last chance to make Mewtwo reconsider his actions before things reached the point of no return. "All of my children are the same in my eyes," he said. "There is no difference whether they were born naturally or cloned. All life is worth the same."

The permanent scowl on Mewtwo's face only became fiercer. "We were created with powers far stronger than the originals." Poised to fight, Mewtwo watched those opposing him cautiously. "That makes us superior in every single way to normal Pokémon."

"That is where you are wrong, Mewtwo. Inside every Pokémon lies the strength that does not come from any special powers that they can learn. Their true strength comes from within them and them alone. If only you understood that. You wouldn't be planning to murder so many innocents."

Charging up another Shadow Ball, Mewtwo scoffed at the Original One's words.

"I don't need your sympathy," he spat, becoming level with Arceus' height. "And my clones don't need their powers to prove their worth." He fired the attack, which Arceus dodged with ease. It then hit the structure that Ash stood on, creating a crater within it.

"I will block all of their special abilities by using my psychic powers. Then we shall see who triumphs," Mewtwo challenged, undeterred. "Go!"

The clones acted like they were shot out of a cannon, charging towards their natural-born counterparts. Lucario stood in front as leader of the group of normal Pokémon and gave a battle cry, leading them towards their clones. Pikachu tried to stop them but his cries fell on deaf ears.

What happened next no one could have prepared for: Pokémon fighting all over the arena while Mewtwo and Mew raged their battle in the air. Fists colliding, claws scratching, headbutts, kicks, and so much more.

Pikachu and Lucario came face to face with their two clones, staring in awe as the clones prepared for battle. The two Pikachu sparking their cheeks threateningly and the two Lucario stood in karate stances. Without warning, the clones struck fast and struck hard. A Force Palm came from the left and hit Troy's Lucario, knocking him back a bit, while a straight kick to the jaw came from the right. Lucario fell to the ground, grabbing his jaw but refusing to fight the duo before him. His only choice was to back away from them towards center field.

Pikachu wasn't having much luck either; one of his two clones hit him with a tackle right off the bat, knocking him back, before the other one came in and sent him flying through the air, landing roughly on the ground.

Nobody could make a sound, they just stared in awe and horror at all the fighting that was going on. All around, Pokémon were now starting to tire out; they were grabbing each other for dear life or collapsing next to each other out of exhaustion.

"Pokémon aren't meant to fight. Not like this," Nurse Joy said, tears almost welling up in her eyes. "What can come out of it?"

Standing right behind her, Neesha answered that question. "Nothing, but pain."

"Why can't Mewtwo understand it's not right to force Pokémon to fight like this?" Brock asked.

Troy, though badly injured, was able to answer his question. "It's because he wants to prove that he has a place in this world. He wants to prove his own worth and that he is not just some Pokémon that was cloned from a Legendary like Mew. But he thinks that genocide is the way to prove it."

"Why?" Misty asked, anguish in her eyes as clear as day. "Pokémon are all living creatures. We share this world together and we are all a part of it. One is not better than the other."

"I wish I knew, Misty. I really do," Troy sighed. "It's a shame that some cannot see that we all share the same things."

The battles continued to rage on. More and more Pokémon were dropping from exhaustion but Troy's Lucario and Pikachu continued to have their paws full with their clones. Lucario was now just blocking his clones' attacks and not retaliating but even he was getting tired. Pikachu was again still refusing to fight his clones, even as they continued knocking him down with tackles and verbal abuse.

"Quit it! Stop!" Troy heard Ash's voice. The group looked behind them to see him climbing over the barrier into the stadium, falling to the ground after he got over. Everybody checked on him to make sure he was ok, which he was.

"We've got to find a way to stop this!" He cried. "This is insanity. This has to stop."

"How?" Brock asked. "Mewtwo doesn't care about anything but proving how powerful the clones are. It's like trying to move an immovable object, it can't be done."

"Well we have to try somehow." Troy got into the conversation. "This can't go on forever."

"I would rather risk my life out in Mewtwo's storm than watch these Pokémon destroy each other," said Nurse Joy, a lost look in her eyes. "I wish there were some way to stop them. I don't know what to do."

"I don't know if they will stop," replied Brock as Ash's Charizard and his clone collapsed to the ground. "They look like they're willing to fight to the death."

"That's a fight...that no one will win." Misty said sadly. It was true, no matter how you looked at it, there really was not going to be a real winner in this if it keeps on.

Troy watched in sadness as Lucario kept taking hit after hit, but never dishing a hit back at his two clones. Lucario had always inspired him the way he always picked his battles, and in turn helped Troy pick his battles wisely. He was such a reliable friend and partner that Troy did not know what he would do without him.

"Someone has to say no to this. Someone has to refuse to fight, like Lucario and Pikachu." Troy said, noticing Pikachu not fighting his two clones at all either.

"I agree," Ash agreed. "They set a good example for the others. Why can't they follow it?"

Before anyone could say another word, Lucario fell to the ground after taking too many kicks and punches to his body. Troy sprang into action without hesitation, running towards his Pokémon.

"Troy, what are you doing?" Ash called after him.

"I've got to help Lucario." His companion, although strong in body and spirit, could only handle so much onslaughter from his two counterparts.

The two clones stood over Lucario, taunting him through speech and body. Lucario was bruised, battered, and had a black eye already from the beating he had been given. Seeing him in such a state tore at Troy's heart, only driving him to run faster. They were just about to go for the kill until a tall shape stepped in front of them with its arms spread wide.

"Stop this!" Troy begged them. "What is this going to prove? We don't have to fight."

The clones looked at him in surprise and shock. Why was this human sticking up for their inferior version? He was a slave to this human and nothing more.

Troy could see his words weren't really getting through to them. "If you want Lucario, you're going to have to go through me."

The clones gave him smirks and tried to go for a double kick but Troy had anticipated their moves and sent them back. It was painful and he'd no doubt have fractures by the end of it, but Lucario was worth more than words could express.

Behind him, Lucario was starting to recover and stand up on his legs. Troy had only a moment to spare and looked back to gave him an assuring look. "I've got your back." Lucario nodded to his trainer, standing beside him so they could take on the clones together with whatever strength he had left. His trainer wouldn't be able to handle much more.

At the middle of the battlefield, Mew and Mewtwo collided with such impact that it blew a dust cloud a couple feet high in every direction, causing everyone to turn away. The shock sent an electrical surge throughout the entire stadium, causing the lights to be shut down and cover the stadium in darkness.

Charging up their strength, the two Pokémon blasted psychic energy towards each other at close range. The two attacks cancelled out and sent the two back to the trainer's boxes. They once again charged up their energy, preparing for one final burst of energy to destroy the other.

Troy was not blind to this and the pieces of debris that'd hit him were a physical reminder. He knew he and Lucario were being pushed back towards the middle of the stadium by the two clones as the two of them blocked attacks, and now he knew how close they were. He and Lucario were sitting psyducks if Mew and Mewtwo sent their psychic energies out now.

A thought crossed Troy's mind. The collision of the two attacks would kill both of them if they were caught in the crossfire. He couldn't let Lucario die if it came down to both of them.

Mew and Mewtwo then released their built up energy towards each other. Troy had to act fast or they both were going to get it.

"Lucario," he said, holding the sadness in his voice. "I'm sorry. I love you. Know that I will always be with you."

Before Lucario could even react, Troy shoved him out of the way and the two energy fields hit him. A bright light emitted from the blast zone as the two attacks collided.

Lucario stared in stunned silence at Troy's sacrifice to save him.

"NO! TROY!" Ash screamed in horror. Misty and Brock hooked their arms around him to try and stop him from running towards him, despite Ash flailing about.

"Ash, no." Brock tried to calm him.

Once the light and smoke cleared, everyone could see Troy glowing a dark pink. He collapsed to his knees and fell to the ground on his back with his left arm next to his head.

"Fool! Trying to stop our battle." Mewtwo stood in disbelief.

Ash had finally broken free from Brock and Misty's holds and ran to where Troy had collapsed, but having the courtesy to remain behind Lucario who watched with stunned silence. Troy was not moving, nor did he show any signs that he was conscious.

"Troy?" Ash asked, hoping for a response.

The dark pink light faded and instead showed Troy as a stone statue.

"Troy, come on. Please." Ash was starting to beg hysterically. "Please. Don't do this to us."

Though it hadn't officially sunk in yet, he was gone. Lucario immediately rushed forward. He shook Troy's body, hoping something would happen, but nothing did happen. Resting his paws on Troy's back and willing energy into his trainer, Lucario tried but the lack of change was tearing away at the Pokémon's heart.

Desperate, Lucario tried to feel for anything that would prove Troy was still alive by using Aura, although it was a complete long shot.

He found nothing at all.

A long howl rented the air, grief permeating the air as he knelt beside the body of his best friend. He wanted the world to know how much Troy meant to him.

Tears streaked down Lucario's face as he cradled Troy's head in his paws. He felt cold, not the comforting warmth that he always emanated. Lucario couldn't help himself anymore and finally broke down crying, his pained cries echoing throughout the stadium.

It was right then and there that the weight of the situation hit Ash. Troy was gone. He was dead. He would not open his eyes anymore and greet them in the morning with that warm, charming smile of his. Lucario would not have his best friend beside him anymore while Ash lost his mentor.

"This is all my fault," Ash blubbered out as he cried into Troy's chest. "I'm so sorry, Troy. Please forgive me." Turning to the heavens, Ash let his agony loose. "TROY!" He collapsed onto his chest and lost it, letting out loud cries that rivaled even Lucario's.

Standing on the other side of the stadium with his clone collapsed beside him, Gengar also mourned the loss of his trainer. Tears rained down from his eyes and the mischievous grin that seemed to always be on his face was gone, replaced by a saddened expression.

Soon all of the other Pokémon started to cry along with him: their tears being transferred to Troy. Lucario and Ash barely noticed this happen, caught in their own grief.

* * *

 _Troy awoke with a bright light almost blinding him. He lifted his hand to block it out as he started to get up._

 _"Am I dead?" He asked himself, though he pretty much knew the answer already._

 _"Yes, you are." A woman's voice came from out of nowhere. Troy looked around for the source of the voice._

 _"Where are you?" He called._

 _Another bright light flashed before him before parting to reveal a woman. She had lovely brown hair, the deepest green eyes that one could get lost in, and such a beauty that could seduce any man._

 _Tears flooded Troy's eyes. He knew this woman like he knew his own face. He had waited for this moment._

 _"Mom!" He cried happily. He rushed to her and embraced her, not wanting to let her go ever again._

 _"My baby boy," his mother cooed affectionately. "I missed you so much. You've gotten so handsome. You're so grown up now. I wish I could have been there to see it."_

 _"I missed you too, Mom," he replied, his sniffles being muffed by the embrace. Troy was sure he would enjoy the afterlife even more now that he was reunited with his mother._

 _Suddenly, Troy's spirit started to disappear. His hands started to become clear and soon his arms._

 _"What's happening? What is going on?" He demanded._

 _"You're being called back." His mother explained. "It seems that your time has not come yet, Troy." A light consumed her until her body was gone._

 _"No, Mom! Wait!" He cried as his whole body started to evaporate._

 _"I love you, Troy," her voice came. "And I always will. We will be together again when your time has come. Remember that I will always be with you."_

* * *

Troy's stone body turned blue, shocking Lucario and Ash, but nothing really seemed to happen. Staring down at his fallen friend, Lucario mumbled his name once more before tears fell out of his eyes.

Suddenly the dark clouds and the sky were turned blue. The dawn must have been approaching. A bright blue light, like it was sent from heaven above, shined down on the middle of the battlefield. After a few more seconds, Troy's body returned to normal. Lucario felt the warmth radiating once again and his Aura was strong once more.

Ash felt Troy start to stir, hearing his moans. He lifted his head from Troy's chest; hope being restored in him as he saw Troy open his eyes. Troy smiled at the two of them.

"You guys," he said affectionately. Lucario embraced him out of pure joy, not wanting to let him go. Tears of happiness ran down Lucario's cheeks as he and his trainer hugged. Troy ran his hand across the back of Lucario's head soothingly.

"It's alright, Lucario." He soothed. "It's alright. I'm back. I'm here."

After what felt like an eternity, Lucario finally let him go. This allowed Troy to turn his attention to Ash, who was wiping tears from his eyes. Troy held out his hand, gesturing for Ash to grab it. Ash did before wrapping his arms around Troy's torso, tears flooding his eyes again. Troy returned the embrace with a smile and a chuckle.

The others reacted with awe and joy at the sight before them. Brock and Misty were happy to see their companion brought back to them while the other three trainers celebrated in their own way: Fergus pumped his fists while Corey and Neesha embraced…until realizing the awkwardness of the situation and separated.

"Now do you see?" Arceus asked Mewtwo, who was still in shock over the events that transpired. "Troy's selfless act to save his Pokémon proves that humans and Pokémon can be friends. We all depend on each other and help each other."

"I see now," Mewtwo responded. "I see now that the circumstances of how we are born are irrelevant. It is what you do with the gift of life that determines who you are and what your worth is."

Using their psychic powers, him and Mew lifted the clones into the air. The trainers all stood at the middle of stadium as they watched this happen, the clones all saying goodbye in their own ways. Lucario and Pikachu's two clones were the last to leave.

Before she could join the others, Mew came down and plucked the Poké Ball that Troy used to capture her with off of his belt. Troy understood her intent on why she did it. She couldn't let anyone know that she had been captured.

Arceus swooped in to their level. "That was a very noble thing you did there, Troy Black," he said. "I cannot think of another who would do that for their Pokémon. You humans, you are such a marvelous species."

Troy smiled as he bowed to the Pokémon. "Thank you. I needed to do what was right."

"That's the spirit," Brock slapped a hand on his shoulder. "One part courageous, three parts reckless."

"I must leave now," said Arceus, who started to fly away. "We will meet again someday, Troy Black." A portal opened and he flew into it.

"Mewtwo, where are you going now?" Troy called to Mewtwo, as he, Mew and the clones started to get out of sight.

"Where I can learn what your heart knows so well," responded Mewtwo. "What transpired here I will always remember. But perhaps for you these events are best forgotten."

Soon a bright white light engulfed the whole stadium and everyone was caught in it. The whole light then engulfed New Island.

* * *

 **Wow that was heavy. PIMC helped me with getting the emotion just right. So yes, Troy did end up taking Ash's place in being hit by Mew and Mewtwo's attacks only this time it was to save Lucario, rather than some impulsive move. I'm sure what you guys will know what Arceus meant when he says that he will see Troy again. Drop a review telling me if the emotions of the** **chapter got to you, or if they didn't that's ok too. Just review. I really do appreciate the reviews I get.**

 **Now we, in the words of Code Lyoko, return to the past.**


	7. Chapter 7

**Hey all. Can't believe this is the last chapter. It has been such a blast writing this story for you all and I love all the love and support you guys have shown it. I want to thank ProcratinationIsMyCrime for being my partner in crime on this. She's been the best I could ever ask for. But for now, just enjoy the final chapter.**

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The storm raged on outside; the waves crashed against the harbor and the rain fell in buckets.

Inside the port building, there was a budding crowd of Pokémon trainers that were determined to reach the ferry for New Island to battle the world's greatest Pokémon trainer. Officer Jenny and the harbor manager stood at the entrance to the harbor, halting the crowd.

"This could be the worst storm ever," said Officer Jenny. "Because of that, the ferry has been canceled."

"You must listen to me," The harbor manager also said. "You have got to find shelter as soon as possible."

Corey, Neesha, and Fergus stood at the front, disappointed looks on their faces. They didn't know exactly why they were there in the first place but they were disappointed at having to miss the ferry.

"Excuse me please," A voice cried out. The crowd parted to reveal Nurse Joy standing there.

"The Pokémon Center will be open as a shelter during this time," she said. "Anyone who needs a place to stay should come with me."

Corey looked at the two next to him, feeling like he had met them before somewhere but he couldn't be too sure.

"Don't I know you guys from somewhere?" He asked.

Fergus and Neesha looked at him like he was crazy but also couldn't help but shake the feeling they had met him before either.

"Not sure," shrugged Neesha.

"Me either." Fergus shook his head before resuming his cocky demeanor. "Fergus P. Richardson's the name."

"Corey Slayzer," The two exchanged handshakes.

Corey picked up his stuff and walked away from the two of them. He noticed Troy sitting with his other companions. Troy met his gaze and the two of them nodded to each other in respect.

"Nurse Joy and Officer Jenny are really great," said Brock as he watched Nurse Joy guide the crowd of trainers to the Pokémon Center. "They just keep getting more beautiful every time I see them."

Troy scoffed. "Is that all you think about, Brock? Sometimes you worry me."

"Hey guys," said Ash. "What are we doing here anyway?"

Come to think of it, why exactly were they here? Troy couldn't remember what it was. One minute they were all having lunch and then all of a sudden they were at the harbor. Why was that?

"I'm not exactly sure about that myself, Ash," Troy replied. "Maybe we were supposed to catch a boat or something. But I do have the weirdest sense of déjà vu, like this all happened before."

"I do too," Brock agreed. "It's so weird."

Suddenly the sound of fangirls screaming permeated the air, causing Troy to groan. Sure enough, there were three girls standing behind him, basking in the sight of the former Kanto champion being in their presence.

"Oh my gosh, it's Troy Black," one of the girls squealed. She shoved a picture of him and a Sharpie into his hand. "Would you sign it please?"

Troy didn't react for a brief second. He wasn't exactly sure what to do. These girls didn't want him to sign their breasts or anything weird like that so it would be fine.

"Sure." He smiled, signing the picture of him before handing it back to the girl. She had the biggest smile on her face as she walked away.

He signed autographs for the two other girls, one of whom tried to sneak him their cell phone number but he politely declined it. As Troy went back to sit down, he noticed Brock's jealous look.

"Come on, Brock, don't be like that." He smirked. "I keep telling you that I can't control who the girls go for."

"That's not a good enough excuse," Brock snapped. "Why can't I get a girl to like me while you get all of the attention?"

"You're hopeless."

Just as it seemed there was going to be a full-blown argument, Misty got in-between them.

"Let's just get something to eat," she suggested. "We're all hungry so that's why you guys are getting short with each other."

"I'm in total agreement with that." Ash nodded his head.

Before the group would get a chance to set off to find food, there came a cry from the door.

"Look, it's a miracle."

The group of friends looked towards the entrance and walked outside to the harbor. The rain had stopped. The skies were clearing up and the sea was smooth and calm once again. You could call it a miracle because of how fast it stopped.

"Well that's a sight for sore eyes," Troy said, breaking the awed silence. "I always love how the sky looks after a big storm."

Standing on the edge of the platform, feeling the waves rock against it rather than smash, Ash and friends took in the beautiful sight. Rays of sunshine tried to peak through the dark, heavy clouds, and the calm sea went on for miles.

"It's so pretty," Misty's eyes sparkled in awe.

"Yeah it sure is." Brock agreed. "Nothing like the aftermath of a huge storm."

Suddenly Ash and Troy thought they saw something flying in the sky. It looked feline-ish and had a long pink tail. Trailing behind it were things sparkling like diamonds as it flew into the clouds.

"What's that?" Ash asked.

"I'm not sure what that was," replied Troy with a shake of his head.

"What's what, guys?" Misty asked as she and Brock gave them curious looks, unsure of what the two of them were talking about. "I don't see anything."

"Nothing except the sky," Brock nodded. "Maybe you guys were just seeing something in the clouds."

"No I don't think that's it," Troy denied. "What do you think, Ash?"

Ash stood with a bit of a grin on his face. Memories of the day he left home to start his journey flooded his mind, as he was sure he saw another rare Pokémon like he did that day.

"The day I left home to start my Pokémon journey, I saw a really rare Pokémon," he said. "And just now I thought I saw another one."

"That's a coincidence," Troy quipped. "I saw one too. Maybe we'll see another one someday."

The group stood staring out at the sky for a few more moments. Without a word, they walked back to the port building so they could continue on their way. Once they got inside, a most bizarre sight greeted them. A kid was running in like he was late for something. He was bent over and breathing heavily.

"What did I miss? Am I late?" He quickly asked. Ash and the gang finally got a good look at him. He wore a red tank top, black pants, a wheel-necklace that looked familiar to Ash and Troy but they couldn't place, and he wore double black wristbands. He also had a short black Afro and skin as dark as his hair.

"Uh no," Ash answered. "You didn't miss anything."

"Ok good," the stranger panted. "I was afraid that I missed something important. There looked like a big crowd here." He then got a good look at the gang, his heart stopping as soon as he set his eyes on Misty. She was the most beautiful girl he had ever seen. His face broke out into a blush but because his face was dark, it couldn't be seen.

"Well hello," He greeted in a smooth and suave way. He grabbed Misty's hand and placed a kiss on it. "And who might you be, pretty one?"

Misty giggled at the young man's attempt to woo her. "I'm Misty," she replied.

"Misty," he crooned. "Such a beautiful name for a pretty young lady like yourself."

Ash cleared his throat to break up the moment. He could instantly tell he didn't like this guy. He seemed like a total hot shot.

"And who might you be?" He asked in a threatening tone.

"Name's Zyon," the stranger replied. "Zyon Webster."

"Like Merriam Webster?" Troy giggled, thinking it was funny.

The stranger, now known as Zyon, gave him a dirty look but shrugged it off. He collected his things off of the floor and looked like he was preparing to leave.

"I gotta go," he said. "I'm sure we will all see each other again soon."

Without another word, he left, but not before giving Misty a small wink. Ash watched him leave. Something about this Zyon character seemed familiar, almost like he had known him before but for some unexplained reason never stuck around in his life.

"Ooh, I think someone likes you." Troy teased Misty.

"Yeah, that would be a first," Brock laughed, before receiving a mallet shot to the head.

Ash was steaming with jealousy. Why was he being jealous over someone showing Misty some attention? It just didn't make sense. She was his friend so it shouldn't bother him.

"Alright guys," Troy broke his thoughts. "Let's go get some food. I know a good place here on the island. They make the best deep dish, everything on it pizza in the entire Kanto region."

"Then what are we waiting for?" Ash exclaimed excitedly. "Let's get going."

"Alright." Troy laughed, ruffling Ash's head.

The group of friends left finally. Wherever their journey would take them next, they were going to do it all together and nothing would get in the way of that.

High above the city, a figure watched the group of friends walk. He was so stupid to believe that all of humanity was evil and wicked, but not those four friends, and the one who showed him what it truly means to live.

Without another moment to spare, the figure flew off to the northwest to his new home, hoping to live in peace and find out what meaning his life has.

 _'So long, Troy Black,'_ He thought. ' _I owe you my entire life.'_

* * *

 **And that is that. Be sure to drop a review saying what you liked best about the story. Zyon is an OC happily donated to me by the core of justice, so thanks a lot. You'll see more of him in an upcoming story. For now, it's so long until next time. Troy now belongs to LEGAL-EAGLE53 so any other stuff about him will come from her.**

 **It's been a good long journey with Troy, having had him in my arsenal for seven years, but I know with her he will be in better hands. Give me your opinions about him so as to see what I can pass on to LEGAL-EAGLE53 so she can deliver what you guys want.**

 **So long everybody...until next time.**


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